There are 5 Greek islands from which you can enter Turkey, Rhodes, Kos, Samos, Chios and Lesvos. The Greek ferry system being what it is, you first need to determine where in Turkey you want to start so you know which Greek island will be your last before you enter Turkey. If you're interested in Fethiye, Bodrum or Marmaris in the south you can get to these easiest from Rhodes, and you can get to Rhodes from several Greek islands, including Crete, Kos and Santorini, although not necessarily on a daily basis. That will depend on when you go. The ferry schedules for Greek island hopping can be found on www.gtp.gr and www.openseas.gr when they've been finalized. Ferries from Greece to Turkey can be found here: http://www.feribot.net/feribot/?lang=en.
A sample itinerary could be Athens>Santorni>Crete>Rhodes, then into Turkey at Bodrum. From Bodrum you would make your way north, stopping wherever your plans take you. I recommend stopping at Selcuk to see the ruins at Ephesus.
A different Itinerary would be Athens>Santorini>Paros>Mykonos>Samos, then into Turkey at Kusadasi, which is close to Ephesus.