Im looking to travel by Ferry from Thira (Santorini) to Mykonos around about October 20th of 2009. All the sites i have found only have Ferries / boats up until early October. I found Aegean Airlines fly from about $125 Euro, but surely there is a boat i can get to save some $$$???

The ferry is operated by Hellenic Seaways. I can only find ferry schedules until October 9 this year. Last year they were operating until October 30 but I think they must have decided that the demand is too low to justify the extension. Of course that can change as the season progresses. Keep checking the HS website for updates.

It might be possible to get to Mykonos by taking a ferry to either Naxos or Paros, then continuing on to Mykonos after changing ferries. That would also be something to keep an eye out for using http://www.openseas.gr/OPENSEAS/index_en.vm and http://www.gtp.gr.

Santorini and Mykonos are on two separate ferry routes. The only link I know of that's still running in October is SeaJet 2, which leaves Paros at 11:10am. The problem will be finding a ferry from Santorini to Paros that arrives early enough for that connection to Mykonos. You may have to take a ferry the day before, and spend a night on Paros.

Keep checking - all the October ferry timetables won't be confirmed until late September.

Im sure that if i break the trip down i will be able to island hop my way from santorini to mykonos and then from mykonos to Athens (Pireaus Port). Worst case scenario im sure that for the right price someone will take us in a boat. Surely i couldnt get stranded on the island???

You won't get stranded on an island! There are regular ferries throughout the winter so that island residents can get back and forth to the mainland, and for food and supplies to be delivered. How else would they survive?

The difference is: once the tourist season is over, ferries are restricted to routes to and from the mainland. To get from Crete to Santorini, for instance, you would go from Crete back to Piraeus, then take another ferry from there to Santorini.

You are lucky in that during the period you are travelling there should still be a link from Paros to Mykonos. Santorini and Paros are on the same regular ferry route to Piraeus, so you can easily get between those two islands. The question is: will there be a ferry leaving Santorini early enough to make a same day connection from Paros to Mykonos? My guess is that you will have to spend a night on Paros enroute.

A better alternative will be to go to Mykonos first, then Santorini. That way you can take the 10am SeaJet 2 from Mykonos to Paros, connecting there with the noon ferry to Santorini.