Hello! To be honest you do not give away much to help us help you other that some travel limitations.
Is Santorini and in general Cyclades a must for you? And has to be islands + Athens? Greece has a very beautiful mainland too. To be honest it is very hard to advice because you do not mention any of your interests. What is your aim? Relaxing by a beach most of the time or taking in ancient sites, or do some watersports, or do hiking, or use a base and take day trips with the car to explore the area or....
What are must-sees or must-dos for you and what you'd rather avoid other that the crowds (I guess this is what you mean by worrying about spending too much time in big tourist centers? Please clarify! )

These are all very good questions . . . . hopefully my answers will help clarify what we're looking for.

So, we have no must-dos or must-sees with respect to the islands. I picked Rhodes because it was conveniently located from Bodrum and so many people on these boards and the Frommers boards have said they loved Rhodes.

We like to do a bit of everything: some beach, some ancient sites, a bit of scuba diving, and some hiking. We're pretty laid back about our travels and don't feel the need to check off any boxes --- we don't mind missing "must see" sites if another place is more relaxed. For us, the most important aspect is finding good food and a relaxed locals-sort-of-place.

The one thing we hate is over-tourism. It's the number one reason why we just don't like Florence --- way too many tourists and packed crowds. If that's what Santorini is going to be like in June, we'd rather skip it and find a more relaxed island. (I'm actually a little worried about traveling in Europe this summer - we've never done Europe in high season before, instead opting to travel in low and shoulder seasons.)

We know that we want to do Athens + islands and not mainland Greece because we're going to be staying in Bulgaria right near the Greek border for about a month so we'll probably do some daytrips into the Greek mainland from there.

Frankly, I think two weeks In Athens is too much but that's just me. There is a reason, usually a good one, that people seem to flock to certain places and in June the crowds shouldn't be too bad, especially if you are willing to travel/visit early in the day.

I think you are missing out if you don't do the so-called "classical tour/itinerary" which includes Corinth, Naphlion, Olympia, and Delphi and these are not places you are going to daytrip to from Bulgaria.

of course there are many other sites but the ones I have mentioned are, IMO, somewhat "defining" in terms of Greece. Just a thought and I hope your trip is wonderful.

Dukey1, Thank you! This is fantastic advice and makes a lot of sense because we're going to be leaving Greece via the Patras ferry to Ancona so seeing the Peloponnese would work perfectly. So, what do you guys think about something like this:

1 week in Rhodes
1 week in Santorini
1 week in Athens
1 week based somewhere in the Peloponnese to do day trips to Olympia, Corinth, and Napfilion, etc.

I know that the major attractions in the Peloponnese are spread all around but it's much easier for the dogs if we are based in an apartment in one place.

rather than stay in Athens I always stay on Aegina which is a small island not far from Piraeus. You can travel over to Piraeus by flying dolphin and easily be in Athens within an hour. It has 2 main 'towns' Aegina town and Agia Marina which are small and only really get busy at weekend when the Athenians visit. The dolphin goes to both.
It means that you can visit Athens for a few hours and then get back to the peace and quiet of the island.
I took tours of the Peleponnese from there and the dolphin also carries on down to the islands of Poros and Hydra.

Santorini has a unique landscape and is something most people concider a must-do, but have in mind that it is maybe the most advertised Greek island along with Mykonos especially for Northern American visitors, and there are many cruise ships docking each day too. Rhodes is touristy up to a point, and unfortunately some areas are taken by large AI hotels, but it is a large island with many different areas and a bit for everyone. Note for comparison that Santorini is tiny while Rhodes is one of the larger Greek islands. Santorini covers only about 73 km2 (28 sq miles) while Rhodes is about 1,400 km2 (541 sq miles)! Furthermore, from Rhodes you can visit some near by islands (very quiet Halki and Symi for example) on regular ferries or organised excursions , while shedules of ordinary ferries do not apply for day trips from Santorini, plus only boat trips are around the island, the caldera and Thirassia island on my knowledge.
Given your interests, I would pick a Cycladic island (if Santorini is a must for you) that can be served as a base to visit Santorini still is a bit more quiet and has plenty to keep you busy. Obvious suggestions are Paros (plus Antiparos) and Naxos. There are boat trips from those islands to Santorini some days per week, plus some interesting boat trips to Small Cyclades and to Mykonos/Delos. Both Paros and Naxos offer scuba diving, lots of hiking, great sandy beaches, good food and are more relaxed than Santorini. Especially Naxos has plenty of Ancient and Venetian ruins,tiny old Byzantine churches and an inland full of traditional small villages, where locals still go on their own ways uninfluenced by tourism and is a joy to explore.
I think one week in Athens is about perfect to take in the major sites, some museums, explore different areas of the city, hike up Philopappos and/or Lycabettus hill to take in the views, maybe take a half day trip to Sounion and maybe a (long) day trip to Delphi/or to an Argosaronic island.
Corynth can be visited when you leave Athens to go on Peloponnese. Nafplion area is a perfect base to take in Mycynae, Tiryns, Epidavrus, Ancient Asine etc. Olympia is on the other side of Peloponnese so I guess you may depart Nafplion area a night earlier and stop in Olympia for an overnight on your way to Patras.

I like the fact you are looking to spend some time in each of your locations in order to really absorb the culture.
Your progression of Islands will take you to Rhodes first and then to Crete. Crete is even larger than Rhodes and frankly it is so big you can find lots of quiet places particularly in the west where in June you will not be innundated by tourists but there will certainly be enough of them around to make it interesting. You can easily spend one or two weeks on West Crete and not see it all.
These pictures were taken in Crete in June
http://travel.webshots.com/album/559511069PIlVxI
From Crete your next logical island is Santorini but I would be surprised if you want to spend more than a couple of days there to see the views but it is very touristy.
Next logical step is Naxos or Paros. I am aNaxos fan but Paros is also lovely. You can spend a week on either of these islands before heading back to Athens.
Naxos also in June
http://travel.webshots.com/album/552001505EYxVYT
Personally I would do about 3 days in Athens and then head to the Peloponnese, there is so much to see. You may need to consider coming to Greece a couple of weeks earlier!
Peloponnese
http://travel.webshots.com/album/552001505EYxVYT

A couple of days in Santorini is enough.Pretty view but only place we went that was over run with tourists, mostly from US, plus the dreaded cruise ship excursion tours.
For longer stays, which is what we did, Chania for two weeks, Napflion for a week. We also spent time on Paros and Naxos which we enjoyed as well as three or four days in Athens.

So, after spending a long time thinking through things and reading many wonderful trip reports, here's what I've come up with:

8 days in Rhodes
3 days in Santorini
9 days in Naxos
7 days in Athens
7 days in the Peloponnese

I like the idea of basing ourselves mostly in Naxos and Rhodes because they both seem a little less overrun than Santorini. What do you guys think?

And where should we base ourselves in the Peloponnese (north or south?)

I loved Naxos, but I think 9 days days is a long time to spend there. I'd split the time between Naxos and Paros, which is an easy ferry ride from Naxos.

I'm not a big fan of Athens, so I think you really only need 4 or 5 days there at the most, unless you're planning day trips to Delphi, Corinth, and/or maybe Hydra. June is still a long way off, but keep in mind that your plans for Athens ( and possibly some other parts of Greece) may have to change depending on what's happening with the terrible political crisis in Greece.

You seem to prefer basing yourself in a few places rather than moving around every few days, and I concur with that. Whether the number of days in any one place are too much or too little is a matter of taste.

Nine days on Naxos would allow you enough time to see the mountain villages, relax on the beaches, and perhaps take day trips to Paros, Mykonos/Delos, or the Minor Cyclades if you wish. Seven days in Athens is too much for many, but you certainly wouldn't run our of things to see and do. If you can, recommend an overnight (or at least day trip) to Delphi.

I wonder, though, if one base in the Peloponnese would allow you to do the area justice? You could base yourself in the Nafplio area, but it would be a long trip from there to visit, e.g. Olympia or Monemvassia. I spent four days in the southern Peloponnese last September, and really enjoyed it. Lots of pretty seaside villages, ancient sites, and beaches the equal of those on any island. Perhaps you could take a few days off your other destinations and have two bases in the Peloponnese.

I suggest you peel a few days off of Rhodes, like reduce to 5, then add those days to Peloponnese as Heimdall suggests. Or, you could split 10-14 days between Paros and Naxos.

Unless you are set on seeing Santorini, you should consider the islands off the coast of Turkey. I really liked Chios. I really want to see Samos and Lesvos. The small island of Nisyros was fantastic. One of my favourite islands to visit is Karpathos. Here is a suggestion:
2 days Nisyros
3 days Rhodes
5 days Karpathos
10 days Crete
10 days Peloponnese
4 days Athens

Chania's suggestion is really good and would give you a proper feel for Greece as every island is different. I've spent weeks on all of the islands on their list apart from Nisyros which I visited as a day trip from Kos. Samos and Lesvos are my favourite two islands in Greece - again both very different but great places to spend a couple of weeks.

Ok maybe skip Nisyros because of the dogs but I am serious. Rhodes, Karpathos, Crete & Pelponnese would more than fill up your time and moving between islands in the Cylcades may not be the best option for your dogs and the time you have. Really consider Karpathos. Also, Samos and Lesvos are just as good options as any of the Cyclades when you are already in that area. You will waste time getting to the Cyclades. They may have to be another trip. Your options are different from the popular Santorini, Naxos etc. which are "yes" fantastic but your other options are also fantastic! Go with meets your logistics.

Something that no one mentioned, and i just realize are the dogs... you did not mention their size....
Just keep in mind that it might be a bit difficult to find hotels to accept 2 dogs...
Unfortunately most resort hotels in Greece are not very pet friendly.... and having two dogs makes it even more difficult...
Booking.com has this extra option, so that you can check which hotels are accepting dogs, but this apples to only one dog...
Having 2 of them means you have to contact the hotelier directly to find out if they will be allowed.

The issue of "dogs" didn't initially register with me either. Clausar makes a very good point about many hotels not accepting dogs, and that will severely limit your choices. Even if they let you stay with your two dogs, they may not allow you to leave them unattended in the room when you go out. If you take the dogs with you when out sightseeing, you won't be able to leave them in your car, because heat builds up to dangerous levels inside vehicles during the day.

Until recently I was a dog owner myself, but always left them in boarding kennels when travelling. Expensive, yes, but kinder to the animals and less trouble for you.

On my experience large package and/or family resorts are more hesitant to host pets or even have strict rules banning them. Smaller hotels, rooms to let and B&Bs are more flexible when it comes to dogs and cats, it is true though that it is a hit or miss on how someone hotelier will react when you simply show up without a reservation. A lot depend on how your dogs behave and their size too. It is sad but true that many hotels have face arrogant guests thinking it is alright to lock their pets in the room all evening while pets are obviously stressed of been in an unfamiliar environment. I have honestly encounter someone doing this in a hotel in a Greek Island and dog was barking for hours each evening, when guest was notified he said that "dog has to be used to it, to be left alone etc, as guest has to travel for more than 3 weeks on the islands". An other time, a lady left her cat unattended and cat really destroyed with her nails all curtains and linery in the room, really not nice. I know those people are a minority, but how could I convenience those hotel owners to accept a pet anymore... A few eejits spoil it for the rest of us.Also note that some hotels are hesitant to book in pets,especially large ones, because although Greek people absolutely love animals, they are more accustomised to have them on outside areas, and when into the house, pets rarely have access in the bedrooms. Most people loath cat or dog hair on their beds, so hoteliers are affraid that hair is not easily removed and this might caused troubles with their future guests.
You do not mention what your accomondation strategy will be, eg booking in advance when deciding on your destinations, or just find accomondation on the go. If you plan not to prebook, I would certainly do some research, find accomondation that might suit you location, price and facilities-wise, then send a few e-mails and ask if pets are allowd or what, so you know which places to look for when on the spot.
I think dogs complicate things but it is not unpossible to do this trip having donne some homework in advance. Lots depends on how well-traveled your dogs are too. If this is going to be a stressful experience for them, then I see no reason to make things difficult for you and them. If they are well-traveled and they adapt nicely, then I see no reason not to have them with you. (always assuming you are a biot flexible and ready to make compromisses to have them with you : ) )

OP should under no circumstance go to Greece without having booked accommodation in advance.
Booking.com gives you the possibility to check which hotels are accepting pets, but as i said before this is referring to one pet only !!!!
Having 2 dogs ( even small ones) means that you will have to ask for permission from each hotelier, and have the confirmation email in written, when you will arrive to the hotel.

It is possible that hotels will charge extra for the dogs !!

Knowing the greek hotels, i would advice you to start searching now for suitable accommodation, as it won't be very easy, especially on small islands.

I have 2 dogs my self ( tiny chihuahuas, 1,4 kg each), so i know exactly what i am talking about. Usually i book private apartments, when i want to take them with me, otherwise i do it as per Heimdalls wise advice, i leave them at a pet kennel, in order to avoid complications.

Leaving the dogs in the room during the day, will be difficult, as rooms will have to be cleaned....
Taking the dogs with you won't be easy either, as they won't be allowed to museums and archeological sites..
Greeks also don't have sympathy for dogs at the beach, especially when they are in the sea, next to children....
That means that it would be better to avoid popular, crowded beaches......

We stayed in Rhodes in June last year and liked it a lot. It is very touristy - especially when the cruise ships come in to port - but Rhodes town is fascinating and you really should spend a couple of days there. We stayed in the utterly delightful Hotel Attiki - http://www.hotelattiki.com/en/home-page-hotel-attiki/ - and would totally recommend it. However, it may not be suitable for dogs.

From there we went to Lindos and stayed in the Three Brothers Studios - http://www.threebrothers-studios.com/accommodation.htm . Cheap, cheerful, clean and perfectly safe. We also stayed in Villa Koki - http://villakoki.com/ - which has gorgeous views of the bay. Lindos is beautiful. Again it might be a bit over-developed for your tastes, but there are no high rise buildings, and there are some super restaurants.

If you travel in June you will probably be all right "winging it" regarding accommodation. We booked Rhodes accommodation ahead of travelling and then took our chances. Be aware that the European soccer championships take place in June and that might mean that tourism will be down.

Finally I would second the posters who advised shorter times in Santorini and Athens (3 days in each is fine), and also to spend a bit of time on Crete - especially around Chania, or perhaps the southern side - maybe Paleochoura - a friendly beach town.

You should go to Santorini for two days, stay at http://www.hotelmargarita.gr/ then up to Paros for a week, stay at www.laselini.com then try Tinos for four days theres a ferry to there from Paros. After that get back to Athens and stay there for twos days max and watch your belongings. From there take a ferry to Spetses for three days, this should give you a good cross-section view of different islands.

Hope you are going to Meteora during your trip! Pretty amazing place!

OP's last post goes back to Feb. 15, so i don't think that there is a point in making further recommendations.

It would be also very interesting to see how OP is going to resolve the problem with the dogs, but i am afraid that we will never find out.

Their trip isn't until June... maybe they went away for a couple of weeks?

Hi all, I'm still here! Sorry for the delay in responding to all of these fantastic comments and suggestions --- I had to put Greek trip planning on hold while dealing with our Turkey travel plans -- we're heading to Turkey next week for almost 2 months!

Anyhow, to answer some of the questions relating to dogs:
(1) We book almost exclusively at vacation apartments because we have the dogs. It's MUCH easier to find pet-friendly vacation rentals than to find hotels and our dogs are also much more comfortable at vacation rentals. That's one of the reasons why we prefer to go a bit slower. Mariha, I totally agree with you --- there are a few idiots out there who ruin it for the rest of us who travel with pets. We try very hard to be respectful of the places where we're traveling - we bring our own drop cloths, sheets, and blankets so that pet hair won't get onto the hotel/house furniture, and we don't leave our dogs alone in an unfamiliar environment until we are absolutely convinced that they are comfortable (it normally takes them about 24 hours to get comfortable though we've found that they prefer fancy hotels like Hiltons and Dorints and will settle down easily in those places within just a few hours. They're not fans of the cheap hotels and won't let us leave them alone when we stay at an Ibis.

Clausar, as far as leaving the dogs in the rooms, because we're staying in apartments/vacation rentals, it's usually not as difficult to leave them and we've only once had a problem in the last 8 months (and that was our fault because we didn't properly wipe their feet in the super muddy London weather and a rug had to be cleaned.) When we stay at hotels, we ask them not to clean our rooms unless we leave with the dogs for a walk (some hotels like Hiltons and Sheratons actually have a 'dogs in room' sign which will notify the maid service not to clean.) We've been VERY pleasantly surprised by how easy it's been to travel across Europe with the dogs --- most countries are super pet-friendly and they don't think anything of us having our dogs with us - even less wealthy countries like Bulgaria. We're frequently able to take them into restaurants with us, as well.

(2) Also, our dogs are super well-traveled --- they've been traveling over the last 8 months with us all across Europe (so far they've been to 11 countries, I think). We have a cocker spaniel and beagle mix so they're medium-sized. We're currently in Bulgaria with them and we brought them over from the US via cruise ship. Yes, I know it sounds crazy but we're having a blast and so are they --- if you're interested in how we're doing it and where they've been, we've got a website all about traveling with pets in Europe here: http://theroadunleashed.com

(3) Some of the things that we've found with respect to Greece and dogs is:
- a lot of vacation rentals will let us keep dogs and bring them in the house but we have to pay extra cleaning charges
- most of the aparthotels (apartment hotels) will allow dogs without any charge but regular old hotels won't allow them
- Expedia.com, Booking.com, and Venere.com all have "pet-friendly" search functions which work quite well

So, with all that out of the way, I took all of your recommendations and this is the final plan:

Coming from Bodrum
1 day in Kos
7 days in Rhodes
4 days in Santorini (we thought about doing this for less based on y'all's suggestions but the place I found wouldn't let us book less than 4 days and we're arriving late at night on the ferry)
7 days Naxos
4 days Athens
10 days Peloponnese (probably based somewhere near Napflion)

We would have loved to see Crete and some of the other islands but we'll have to save them for our next trip to Greece!

Oh - and we'll probably do a daytrip to Paros from Naxos since we have so much time there. I think the other islands might be too far for daytrips.

I haven't check your link yet, but I'll have a look as soon as possible.
I am sure you'll have a great trip! This is a very well-structured itinerary : )

I know I am biased but I think you will be happy in keeping your Athens stay at four days/nights. I know there is much to see and do but we had only three days/nights there and after we got into the countryside were delighted with the lack of noise and diesel fumes.