Ferry schedules for that part of the year have not been approved by the autorities yet. In particular, the route Heraklion-Santorini is a seasonal one and for the last X mymber of years it has only been "active" from around Easter to mid-September. Try a mock booking on Seajets' site: When I try July or June it looks for availability, etc. When I look for October it simply does... nothing. I'm not trying to convince you to go through the Peloponnese, but just to find alternative ways of going to Santorini durting that time of the year, which are still very, very nice.

There are few train lines in Greece and those on the mainland have been hit hardly by the floods last September; they function at much less than 50% capacity at this time. The line on the Peloponnese also has a very reduced schedule. Buses are the only alternative to a rental car. Have you thought of renting one-way in Heraklion or Chania and after your week on Crete (where a car offers a lot of possibilities) sailing from Kythira (yes, this route functions throughout the year), visiting tha amazing Peloponnese (including the sexy town of Nafplion and the area, as suggested by David55) and returning the car at ATH from where you can fly to Santorini?

Lots of possibilities, even if in October the Crete-Cyclades ferry line is not available