Because of the early departure from Heraklion to Santorini yes, you will have to get up early. You can either rent a car from an agency in Chania with a dropoff agency in Heraklion or you can take the early bus, which would drop you off at the port. Depending on your day of travel there might be two ferries to Santorini but they both depart around the same time. Once you get to Santorini you can take the port bus into Fira and then another the rest of the way to Oia or you can hire a taxi or reserve space on a shuttle van. Taxi and van will cost around €25 one-way for 2 people. I'm pretty sure Andronis also offers a private transfer.

You can safely buy your ferry tickets to Santorini once you're in Chania.

http://tinyurl.com/3mvhgf9

http://www.a2btransfers.com/en/GREECE/SANTORINI

http://www.santorinitransfer.com/santorini-taxi-rates.html

If you find a hotel you like at St. George Beach on Naxos you will be within easy walking distance of everything Naxos Town has to offer. Just know that Naxos is not "a smaller island" by far. It's actually the largest island in the region. If you want small, instead of Naxos take the ferry from Santorini to Paros and catch the next local shuttle ferry to Antiparos. They leave very frequently from the same wharf.

Arriving at Noon in Athens allows you to catch an ongoing flight out to Santorini that same day. Save all of Athens for the end of the trip so you can relax there and not have to stress about returning to the mainland for your flight home.

Well, I can answer a couple:

Heraklion is the only port with daily ferries to Santorini, and they all leave in the morning. Actually there are only two companies: Hellenic Seaways and Sea Jets Consortium, and the former would be my preference. There is also a once per week conventional ferry leaving early afternoon on Sundays. Don't worry about booking ferries yet — the timetables will be out in spring/summer, and you should have no problem getting tickets, even if you wait until you are in Greece. For Santorini to Naxos there is a daily Blue Star ferry, and it is never full. That's the one I would recommend, and you can buy your tickets when you get to Santorini.

The best beaches on Naxos are in the stretch from Agios Prokopios, Plaka, and beyond, but for the last half of September it would be better to stay in Naxos Town. The St George area of Naxos Town has many rooms, hotels, and apartments, and it's only a 10 minute walk into the harbour/kastro area where most of the shops and restaurants are. It is easy to catch a bus to Agios Prokopios or Plaka for a swim, but you will need a car to get to the more remote beaches. A car would also be handy for exploring the beautiful mountain villages of the island.

BLL posted while I was composing my reply, and I agree with what he wrote. Naxos is much bigger than Santorini, but most visitors stick to the small area of the island around Naxos Town and the SW coast beaches. The mountain villages are well worth visiting, but few tourists stay there.

Antiparos, as BLL knows, is my favourite island. It is very quiet in the last half of September, but most hotels, shops, and tavernas stay open until the end of the month. If you want an island where you can walk everywhere, and have a choice of half a dozen beaches you can reach on foot, that would be a good choice. Get off the ferry at Parikia, the Paros port, and there will probably be an excursion boat ready to take you to Antiparos. If not, there are buses to Pounta where the car ferry leaves for Antiparos every half hour or so.

Thanks for the information! Hopefully it won't be too hard to get from Chania to Santorini. Has anyone else done this or have any more advice on how to do it smoothly?

We thought about going straight from Athens to Crete but decided we would probably need a day to relax and get ready for the rest of the trip. We hope to just catch a flight the following day into Chania Town. will we have any trouble getting from Naxos back to Athens?

Thanks again for helping the more advice the better!

If you have a choice on the ferry between Heraklion and Santorini go with the Hellenic Seaways FlyingCat4. SeaJets has a poor reputation for reliability and a history of breakdowns.

I urge you to reconsider spending your first night in Athens. A flight to Chania only takes a little more than an hour. Better to relax there than to have to make your way into Athens and back out to the airport the next day. You'll waste valuable relaxation time if you do.

Thanks Heimdall for the info on Antiparos, I have heard many good things. Would you suggest Antiparos over Naxos? We love visiting beautiful beaches especially when they are remote. Are there decent restaurants in Antiparos? Could we still get back to Athens easily?

I also wanted to know what Oia is like in mid-September. We are hoping that most of the crowds will die down a little by then.

Let me pitch in again: it takes just about as long to get from the airport to central Athens as it does to fly from there to Chania. Going directly to Crete will save you a trip into the city and one check in/check out of a hotel. You will gain an extra day on the islands.

It's easy to get from Naxos to Athens. There will be two Blue Star ferries, one in the morning and one in the afternoon. Possibly also a Hellenic Seaways highspeed, but it's too early to know for sure. Naxos has a small airport served by Olympic Air Dash 8-100 aircraft, usually one flight per day.

I think you all have made a very good point about Athens that I had not thought about. I think that we will indeed head straight to Crete from Athens. Thanks for clearing that up for me,

We stayed at Hotel Spiros on Naxos and loved it. I don't see your budget but I may have missed it, but we found it affordable http://www.hotelspiros.com/

We are all cross-posting. Yes, Antiparos has many good restaurants, and the beaches are sandy with pebbles mixed in. Most of the beaches are small coves which are good for snorkelling. For that reason I prefer them to the long sandy beaches of Naxos. If you just want some relaxing days on the beach and pleasant evenings in town, Antiparos is great.

If you rent a car you could stay in San Georgio, a small settlement at the south end of the island, an area consisting mostly of expensive villas and some great beaches. See http://www.dolphinantiparos.gr.

If you would rather not rent a car it would be better to stay in the town, where everything is accessible on foot. You have a choice of several beaches, some organised and others not. There is even a clothing optional beach at the north of the island (15 min walk from town) where you can wade/swim to the uninhabited island of Diplo, and have the entire island to yourself.

We visited Oia in late September and it was pretty crowded, mostly Americans unlike the other islands.
Make reservations for dinners, rent a car for a day or two to explore more of the island and it will be OK.

We enjoyed our several night stay in Piso Livadi on Paros. We stumbled upon Kohili Studios (we had no reservation), which is a short walk from the main area. Several of the rooms overlook the ocean, and there is a private beach. The rooms also have kitchens, so we were able to cook our own private dinners on some evenings.

There are also many hotels along the main beach area, if you prefer that.

The best and most affordable food we had in Greece was in Chania (and Crete in general - we also spent several nights in Heraklion before heading to Santorini).

Antiparos has plenty of restaurants with outdoor dining and several by the harbor. We enjoyed Antiparos very much last year and can see why there are so many return guests. Our hotel was Kouros Village in the harbor. Great location, simple lodging but clean with a lovely terrace overlooking the harbor. It's easy to get around Antiparos without a car until you venture out to see the other side of the island which is not far.

For me, Naxos gave us the beaches we enjoy but a car was needed. Plaka beach was beautiful with clear water and sandy beaches. We stayed at Nissaki Beach Hotel, which is very nice. However, the beach quality isn't the same as Plaka and at the end where Nissaki is located is murky. However, there are a lot of cafes along the beach so many places to walk to for dinner or sunset cocktails.

This is one area of Plaka beach we enjoyed. The website has photos of the beach that may be of interest. It was great for a day trip to relax by the ocean, nice lunch from the hotel lounges to rent.
http://www.medusaresort.gr/location.htm

Echoing the suggestions from the Greece experts to continue on to Crete from Athens and save your exploration of Athens for the end.

By mid-September the crowds have thinned significantly but because of its popularity Oia is still busy, relative to the tourist influx at that time of year. You'll get the cruise ship bus tours in the late morning and some for the evening sunset, but the rest of the day is very nice.

Good to hear, it sounds like it wont be as busy as the summer months which is nice. We were thinking of doing a sailing trip on Santorini, but would be open for any other suggestions anyone might have.

As for the 4-5 days we will have in the Chania Town area of Crete, any "can't miss" day trips that we should make?

I'm still a little torn between Antiparos and Naxos but it sounds like we can't go wrong with either. Our budget would most likely be 100-150 per night USD in Naxos/Antiparos.

If you twisted my arm right now I would have to choose Antiparos over Naxos and we enjoyed Naxos. But, I was going back over our photos and remembering what a fantastic time we had at both islands but.... Antiparos had something. It is charming, friendly, and beautiful. And, it easily fits in your budget.

You can't go wrong with either choice.

Hi Mike0611,
While in Chania, go to Falassarna - a great beach on western Crete by car or bus.
I you have time drive to the south coast - truly worth it!
I think the first night in Athens is a great idea after the long haul flight from US.
Pay homage to the Parthenon and stroll the Plaka.
View the lights on the Acropolis after dark and get a good nights sleep.
Antiparos is wonderful, but transport will take longer to get there for sure. Sounds like you only have 4 days in the center of the Cyclades. Stay on Paros and you have wonderful beaches. You can easily take a day trip to Antiparos or Naxos from there.
Enjoy your honeymoon!