There are no ferries between Istanbul and the Greek Islands, but there are ferries from other Turkish port cities to some of the Greek Islands. Check this website:
Right now there's one ferry a week on Sundays between Santorini and Amorgos. Go to www.gtp.gr and use the "Ferry Schedules (Domestic)" function to check for updates. Schedules appear only about 4-6 weeks before any given departure date.
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