Glad to hear that some other Americans are appreciating Samos ... I've visited 3x, twice as a "pass-through" link, and once as the "switching center" for quick trips to Ephesus, Patmos AND Chios. If you are going back there to make a connection from Vathy, I recommend the simple hotel about 400 meters along the water from the quay - Hotel Pythagoras. Balconies on the bay. A restaurant next door (can't recall its name!) with tables only feet above the water, and stunning view of sunset in mouth of Vathy Bay. If your ferry schedule means you'll stay a day in Vathy, its museum is the best in the N.E. Aegean. Of course its kouros is famous as the Largest in the World (they built a room for the headless statue, then had to put in a raised skylight when they found the head!). But don't overlook the side room full of small beautiful offerings found at excavation of Temple of Hera.
Also think u will enjoy Amorgos. I found Katapola to lack much charm, but loved Aegali ... the beach there is sandy & nice and relatively noncommercial (half a dozen years ago, NO sunbed rental, and beyond a low stone wall, grazing donkeys!). A good budget place just off the beach -- the simple lodgings Askas Pension. Askas also has a campground in a wooded area adjacent, but not noticeable off-season, I found. Aegali very small, best taverna is called Katerina's by the locals, don't know if that's its official name, it's under a big flowering tree, always has customers. Above Aegali are 2 lovely mountain villages -- you can take a bus up to one then walk from one to the other. The one to the right (facing the mountain) has a super taverna called Nikolas'... I treasure a sunset picture of us at table, background, down mountain to beach & sea. Be sure to catch last bus 9pm, no fun to wals down road in dark. Island Bus service very limited ... we caught a bus up to Chora (GORGEOUS), wandered around, then decided to walk down to the church by the water... had to cross steep downhill grazing-grounds of goats, finally gave up short of our goal because we stupidly tried to do this in heat of the day. Better to rent a car, or get a taxi to church; I believe busses stop down there every couple of hours. Scenery is Spectacular! I've been on 25 islands, can't recall many as dramatic ... peaks, abysses, the winding road from Aegali to Katapola has u holding your breath.
If you do stop in Mykonos to make a connnection, and don't plan on a posh hotel with pool, you might enjoy a night's stay at a quiet convenient spot in town, uphill just a bit from the nightlife, at a quiet place run by an American ex-pat artist ... Angela's Rooms ... a rose-decked building in a garden, just behind Hotel Despotika. about 100 yards along the road uphill from the main Bus Square, inland from the port. balconies, fridges, a/c, good beds, the usual -- but ALSO the best showers/bathrooms in a budget place you probably will encounter on your trip (she's from US after all).
It sounds as if you're being flexible with your itinerary, which did not mention total time-frame. As I'm sure you have found, there is no need to book ahead on ferries in this season. Enjoy the rest of your adventure!