Samos to other Greek Islands?

You have MANY options. Go to www.gtp.gr and where you see "Ferry Schedules-Domestic" enter Samos in the "From" box. Leave the "To" box blank and clik "Go". On the next page choose June 1 as your date and clik "Search". On the next page you'll see a dropdown menu with all the destinations you can reach from Samos. Samos has 2 ports, Vathi and Karlovassi. From Kusadasi you will be arriving at Vathi. Don't expect all the schedules for June to be visible yet. That won't happen for around 6 weeks or so.

What I have found helpful is Thomas Cook's Greek Island Hopping Guide. See if you can find a copy of at the library, even if it's outdated. It has maps in the back that show how all the islands are connected by ferries. The ferry schedules may not be accurate as far as days or times, but it will show you approximately what you will be able to do. Then, when the ferry schedules come out, you can firm up your plans. As for which islands to choose, it depends on what you're looking for. Read the descriptions in the Thomas Cook book, and look up Matt Barrett's Greece website. You may be able to get to Mykonos from Samos, if that sounds appealing. Or if you are looking for smaller, less touristy islands, you might consider Ikaria or Patmos. On the way from Samos to Ikaria you will pass through the Fourni Islands, which are tiny and looked really appealing to us. We wish we could have spent a couple of days there. You could visit Fourni, then Ikaria, then get back on the ferry and go on to Athens. If you go to Patmos, you can continue south to Leros, another little-visited island. From Leros you may want to fly back to Athens. Or if you have more time, continue on down the Dodecanese to Kos or Rhodes and fly back to Athens from there. Lots of options!

Many Thanks for your very helpful information! I ordered an older copy of Greek Island Hopping for a dollar + S+H through Amazon. Because we will be island hopping the first week of June, do you think we could find flights the day we wanted to fly to Athens? If that's possible, we could leave our decision about when to go to Athens and from which island until we're ready.I truly appreciate the island suggestions that you made! Joy

Because both Olympic and Aegean fly between Athens and most Greek islands your chances are very good in early June for a last-minute flight. The price might not be as low as you'd like, however. You won't know what it is until you're there.

You could wait until the last minute, but I would recommend buying your tickets as soon as you have a final island in mind. You might be able to save some money (right now Olympic Air has "Economy Smart" tickets from Samos to Athens for 43€ at 12:10 pm on June 8, but only 3 remaining; when they're gone, the price almost doubles to 82€, and can go as high as as 128€). But more importantly, you'll have peace of mind: if you end up on Ikaria, there's only one flight a day, and a limited ferry schedule.
You could maintain some of the flexibility that you want by not booking all of your hotels in advance. Thus you could spend more or less time on each island depending on how you like it. But you should still allow a minimum of 2 nights (which would be 1 full day) per island. I guess I should have asked ... how many nights do you have between landing on Samos and your flight home from Athens? Also, is this your first visit to Athens? If so, you will want at least 2 nights (1 full day) in Athens before your flight home. Logistics get a little more complicated in these lesser-visited islands, but they can be well worth it.