I strongly suggest using the Greek travel agencies on my site to book hotels, particularly if you plan on going to more than one island and will need to make a ferry connection.
Many hotels on the internet are offering special rates to book directly with them, but they won’t help you with the ferries and if you can’t get to the island because there is no ferry you still have to pay for the room.
If you book with the agency, getting you to the island becomes their responsibility. It makes traveling a whole lot easier and a lot less stressful when you don’t have to spend hours searching for accurate ferry or flight information.
People who use the automated booking sites often have problems connecting the islands they have booked hotels on to the existing ferries.
Work with a knowledgeable human at a reliable Greek travel agency and don’t be afraid to ask questions.