I would take the ferry from Samos right back to Athens personally. It's been a few years since I sailed that route but I think that bit would be more frequent/predictable than a route from Samos to another island. Sure, it's a long journey (9 to 11 hrs) but you can make it comfortable. Get a cabin, some food and a good bottle of wine and enjoy the trip. If you haven't taken an overnight Greek ferry before it's actually a bit of a cultural experience and an insight into what makes the country tick in winter.

Another option, since you'll be able to cancel your entire return trip for free: you might find a ferry to Turkey (it's literally 1.5km between Samos and the Turkish mainland). I think they may only run in summer for tourists, but you never know. You could then get to Izmir and fly back from there (still via ATH if you want the segments). Ha that's just me coming up with an adventurous option - I'm the guy who never flies direct when I could stop off somewhere weird and new.

Anyway, there is some time yet. The winter ferry schedules should be out in early September. You can decide then, as no flight or ferry will be fully booked in November.