I would suggest booking the hotel asap, but just be aware of cancellation policies. IME, most places can be canceled within 24-48 hours without penalty.

The ferry schedules will come out a few weeks ahead of time. If by some chance there is no ferry on the day you want, then you can try to modify your hotel bookings. But no way would I wait to book a hotel until the schedules come out. Certainly not for Santorini in late June. Some places are very small, just a few rooms, and get booked very early.

PS -- I traveled by Blue Star ferry from Naxos to Santorini in early June and I do recommend that method of arriving. The views are pretty spectacular coming in through the caldera, and the Blue Star is a fun experience by itself imho. I enjoyed it a lot more than the high speed catamaran, or whatever it was.

The Blue Star car ferry is a daily ferry all year long. It arrives at Paros from Athens around Noon and departs for Naxos and Santorini soon thereafter. You will reach Santorini at approximately 3:30pm.

There will be other ferry options on that same day as well but this one is the one that allows you to stand out on deck as you enter the caldera at Santorini.

The no-sail Wednesdays that are mentioned most on these forums (fora?) are the fast-ferry from Heraklion Crete to Santorini. Not Naxos.

Go ahead and make your hotel reservations and don't worry about the ferry. As brotherleelove wrote, Blue Star is a daily ferry, and is already showing up on the http://www.bluestarferries.com/ website, possibly not available for booking yet. There will be other ferries as well, but I agree that this is the best one to take.

If you have a firm travel date, you may wish to prebook the ferry tickets, but you have plenty of time to do so, as ferries are rarely full in June. Personally I would wait until arriving in Greece to buy the tickets, but for peace of mind you may wish to book over the internet. If you do, you will be given a reference number to pick up the tickets at a Blue Star agent.

I will add that the Blue Star ferry seldom fills up so purchasing tickets in advance of your arrival on Paros and Santorini isn't necessary. You can buy tickets for Paros from the Athens Airport desk of Amphitrion Holidays in the Arrivals Hall between exit/entry doors 2&3, and once you're on Paros and ready to move on to Santorini you can buy them from a ticket agent on Paros. Buying your Paros tickets at the airport eliminates the pressure and chaos of dealing with the crowds at the Piraeus ferry port.

Great advice everyone. Thanks a lot. I can go ahead and book my hotels now.

Please visit the more important places on your wish list first
Last time when I was in Greece, there was a strike of the ferry companies and I had to spend 2 extra days at Santorini and give up plans of going to Mikonos. ( which was a blessing in disguise) But some ferry got canceled and I even had to spend an extra day at Crete. Be flexible when you are in Greece.
Overnight ferry to Santorini was very nice and comfortable. if you take that one, you save a day You can see the same Caldera view while departing; which I feel is just OK compared the the other dramatic visuals you will be exposed to, at Santorini.
I must say one thing about Santorini. I saw it lot of pictures, read a lot about it. I was expecting a certain awe factor and had prepared myself mentally for it. But even after that, Santorini still managed to surpass all my expectations and anticipations. One can travel thousands of miles just to watch the sunset from there. We met many tourists endorsing my feeling, who had done that several times in their life span.
Have a memorable holiday...

In my research I have Blue Star ferry leaving Paros daily in high season at 11:45 am, arriving Santorini 15:20 pm.

Paragkash, can you please elaborate more on the overnight ferry? Is it akin to traveling on overnight trains?

Am planning a trip to Santorini in mid-June 2011.

I can help with that. There are sleeping cabins, indoor snackbars, economy and VIP lounges and indoor as well as on-deck seating areas. Here's a photo gallery for the Blue Star ferries:

http://www.bluestarferries.com/site/content.asp?sel=668&loc=2

Indiancouple,
You already have your answer I believe. I will add however, that I always book my hotels as soon as I decide to be sure to get the lodging I want and have never had trouble getting connections in June and July. You'll be fine getting to Paros and Santorini as they are on main ferry routes. Enjoy!

Thanks parosblue. I have finished my hotel bookings for Athens, Paros, Nafplio, Cappadocia and Istanbul. Only Santorini remains, which I hope to wrap up within 1-2 days. I now realize that I will have plenty of ferry options between these islands in late June.

Thanks for the info on the overnight travel to Santorini, brotherleelove2004.

What is the easiest way to get from the airport to the Blue Star Ferry station? I've taken the subway from the airport to downtown Athens but I have not taken it to Piraeus.

Also can you recommend a decent and inexpensive hotel (around 50 to 75 Euros) in Santorini that is close to the main tourist areas? It doesn't have to be near everything.

Thanks again.

minstainy, if you want brotherleelove's excellent advice on lodgings (he is THE top expert on this on all the Greece forums), you must give him the essential mssing fact --WHEN? 75 Euros buys a whole lot more in May or September than it does in high season (July-August).

There is an Airport Express Bus (X96) that leaves the airport every 30 minutes or so for the ferry port of Piraeus. The Blue Star docks are very close to the bus stop in Piraeus. Buy your ticket at the kiosk outside Door 5 on the Arrivals level. The trip takes about 75 minutes unless there's a traffic jam. The fare is €3.2 and there's a ticket validation machine inside the bus as well as ample space for luggage storage.

Fira is Santorini's main tourist area. Check the websites for Villa Fotini, Villa Popi, Pension Petros, Villa Anemone, Summertime Pension.