Greece - mid July Athens, Naxos & Santorini

On such a short trip the most precious commodity is time not money. If you can fly directly to Santorini then you don't have to put in the hours in Athens that first night nor have to commute into Athens then back out to the airport the next day. Ferry travel to Naxos takes about 5 hours and to Santorini about 7.5 hours. Fast ferries are as expensive as flying.
Being cost conscious should never trump maximizing your time on your chosen destination.

Santorini is all about the view of the Caldera. Hotels with that view are very expensive but to my way of thinking worth the cost. You can get far less expensive hotels but without the view. You can stay near or in Fira the capital which is quite busy, Oia is the lovely village on the caldera at the far end of the island. Both can be crazy with cruise ship crowds.
I would look for a hotel in Firostephani which is a short walk from fira but just far enough away that the cruisers don't go there.
Go to booking dot com and punch in your dates and Santroini and it will give you prices availability and reviews. Any hotel with an 8 rating will be a good one. Filter by lowest price first so you can see budget hotels.
Santorini http://www.flickr.com/photos/stanbr54/sets/72157632154800782/

The ferry trip to Naxos takes 2.5 hours. I believe the first fast ferry (Championjet 1, last year) departs Santorini by late morning and will get you to Naxos by about 1:00 as I recall. The wonderful Blue Star conventional ferry won't get you to Naxos until late afternoon. Again this is a matter of spending money to get you to your next destination faster. Championjet by the way has an open rear deck so you can be outside to experience the breathtaking departure from Santorini.

Naxos is the perfect companion island to Santorini. It has the same white and blue buildings, a lovely main town and great beaches all at less than half the price you are going to pay on Santorini.
I would suggest you look for hotels at St George beach. It is part of Naxos town so it gives you a beach holiday with all the advantages of the town. Its a 10 minute stroll into the main waterfront promenade.
Naxos can easily take up a full week.

Naxos Town http://www.flickr.com/photos/stanbr54/sets/72157632094558042/
Trip around Naxos http://www.flickr.com/photos/stanbr54/sets/72157634605629689/

If you are using booking dot com its Agios Georgios.

We choose inexpensive studio apartments with cooking facilities for breakfast and snacks. You can get sea view for 50 to 60 euros. Look at Diogenes Studios, Studios Naxos. Sigma Illiion. For a real treat look at Boutique Hotel Glaros. Not in the same price range but beautiful. Hotel Spiros is also a favourite.
St George Beach Hotels Naxos http://www.flickr.com/photos/stanbr54/sets/72157632162394787/
St George Beach Naxos http://www.flickr.com/photos/stanbr54/sets/72157632113170279/

You can take excursion boats to the little cyclades islands and to Delos Mykonos which is an important archeological site.
It is possible to visit Paros using the conventional ferry system. Its the only realistic day trip by ferry.

Athens probably needs two or three days to thoroughly visit all the sites around the acropolis and Athens center.
Athens http://www.flickr.com/photos/stanbr54/sets/72157632121475515/

Going to Santorini for one night is a waste of time. It's one of the most popular and heavily touristed islands in Greece and may or may not give you what you want for a Greek Island Experience.

Spend your time on Naxos, one of the best of the Greek Islands with a wonderful combination of Old & New World Greece. Naxos Town offers a lovely waterfront and Old Town with a mix of touristy and non-touristy shops, markets and taverns. We stayed in St. George Beach just a short walk from the Old Town and a lot more quieter with more atmosphere.

You can day day cruises to Delos/Mykonos (Delos is wonderful Mykonos is a smaller version of over-the-top Santorini), or a day cruise to Santorini which will give you the experience of Santorini without the higher costs and crowds.

You can also do day trips from Naxos to the Small Cyclades Islands with more tradition and "Greekness" than big name Greek Islands.

Or just stay on Naxos and explore a beautiful island filled with archeological/historic sites, centuries-old Byzantine churches, villages cascading down mountain sides, great food, wonderful locals and a more "true" feel for a Greek Island.

Dana -- I agree that time and convenience is worth a lot, for a short vacation like this, so I would recommend biting the bullet and flying directly from Prague to Santorini.

Check cruise ship schedules for Santorini for the day(s) you plan to be there. July 9 and 10 actually look pretty empty at this point (although that could change) so you might consider 2 nights on Santorini if you can find affordable lodging.

I concur with staying on St. George Beach in Naxos. We stayed at Studio Kalergis right on the beach, which was great. At the far end of the beach -- opposite the town -- is Flisvos Sportscenter. They have windsurfers and jet skis for rent which you and your daughter might enjoy. If not for the water toys, at least walk down there to enjoy a gorgeous sunset from the Flisvos front porch or its comfy cushions on the sand.

On another day, you will want to get into the interior of Naxos to see some of the sights of the island. You can rent a car for a day, or take a bus, or even a taxi. I think you'd enjoy the day trip to Mykonos and Delos as well.

I hope you have a wonderful time in Greece!

Thanks so much. Great ideas!!