You will certainly have no problem with transportation. Do not worry about that! I agree with theodoridi about the prices. They are really lower this time of year! But remember that on 8th of April is the Orthodox Easter and you may have a problem with accommodation! If I were you I would book the rooms now just to be sure!
For the time period you are coming to Greece you can visit more than 6 islands. Have you thought of visiting central Greece? You will be surprised! For accommodation have a look at http://www.r4u.gr
(only for Greek hotels).