If you are booking directly with the hotels keep in mind that if you can't reach the hotel because there is no ferry when you thought there was one and you can't get to the island you will most likely still be chared for the room. I strongly recommend that unless you are a backpacker staying in campsites or are prepared to stay anywhere you find upon arrival, use a travel agency in Athens to book your hotels on the islands. They can get the schedules and won't book a hotel for a day that there is no boat. If you are going to more than one island this is especially true. If you think it is hard getting the schedules from Pireaus try getting them for the boats that go between the islands.
Many agencies offer island combinations.
It is not a tour. These itineraries are set up individually and you can choose the hotels and the islands. Be your own ferry. Rent a sailboat. A one week trip will cost about the same as staying in a hotel and it's a lot more fun.