Greece / Turkey Advice

I think the best method would be for you to buy an "open jaw" ticket. Fly into Istanbul, make your way south to Ephesus, ferry across to Samos, a Greek island, then fly to Santorini (with a plane change in Athens) or use the ferry system to get you to Santorini (time-consuming, probably 2 days), then return to Athens for your flight home. This prevents backtracking and gets you back to the mainland for a couple of days in Athens so you don't have a last-minute scramble to catch that flight. One other option, if your timing is right, would be to take a bus from Ephesus south to Bodrum or Marmaris where you would catch a ferry to Rhodes in time to catch a ferry to Santorini. The challenge is the timing. That ferry only runs 3 days/week. There may also be another company once a week. Greek Ferry Schedules Here You won't find ferry schedules for next September for a few months yet so flying from Samos is your only realistic option if you're planning your bookings now.

This is definitely doable. I would agree on flying open-jawed, especially here. We travelled at the same time of year 2 yrs ago for 3 wks. We flew into Istanbul, saw Turkey, then took the ferry to the Greek isles (Samos) from Kusadasi. (In between, we flew to Capodoccia, then to Ephesus and Pamukkale via Izmir, then to Kudsadasi.) The ferry system can bog you down as it can be difficult making connections. There are no direct ferries from Samos to Santorini. We had to spend a night in Kusadasi we did not plan on, and had to spend another night on another island to get to Santorini. We couldn't find flights that worked for us, but the suggestion to fly to Santorini may be a good one.
I would suggest the overnight ferry from Santorini to Athens if you go by ferry. It made up a night for us as we arrived early in the morning in Athens, saving a night in a hotel.

We have done Greece - what we did was fly between Santorini and Athens (Aegean Airlines or Olympic Airlines have daily services). Santorini to Athens is a bit too long by ferry - so would not advise you to do it.