Months to avoid: July/August, when mega-planes arrive & dump all of N. Europe on the isles, jam-packing them. Also, it's MAJOR hot, mid-day can be 100°F. Aside from that, May-June and September are the faves, temps are ideal. I myself like late May into late June ... rains are gone but the "green" isles are still lush, everything's open, nothing's crowded, Greeks have time to socialize with you (and they LOVE to talk!) ... you get more for your $$, room rates lower, also u get 1 1/2 days for every day because sun doesn't set till nearly 9 pm. Only thing, water is a little brisk until late May, but unless you're from deep South US, it's just fine. In Sept, water is divinely warm, BUT, without rain for 4 months, things begin to look a bit dry/brown, and also-- the Greeks are a bit burned-out after high-season mobs, & are getting ready to close shop & get their kids in school, so a bit different mood from June.
Ferry service? May is "transition time"; service more frequent after June 1, tho still some last-minute changes. However, if you stick to major ferry routes, you'll be Fine. Most Greek Isle newcomers from US start with the cycladic islands ... just don't stick the the US-favored cliche of Santorini-Mykonos. Other nearby isles to consider depending on your interests, include Naxos, Paros, Sifnos, Ios, Milos, Folegandros. But don't ask us to recommend when we know nothing of your priorities. Here's a good online Overview by a young greek guy who llikes both ruins AND beaches, culture AND nightlife: http://www.greek-islands.us ... I also recommend gooing to Library & getting "GREEK ISLAND HOPPING" -- best book for planning a 2-week budget trip. & also advice on managing the ferry routine. BTW, if you want to maximize your fun time and minimize travel time, consider choosing a flight that arrives in AM so that on arrival in ATH airport you can jump on a domestic flight o your farthest island (cost less than $90 if you get a "bargain" flight rate), then you waste no time getting to an island & reliving. Enjoy your planning.