After rereading the original post. I think you should cross off Boston and the cape. You simply can't do all that with just 2-3 hours sailing per day. There are plenty of ways you can fill 4 weeks just in LI and BI sound and the cape Islands. Plenty to do and see Dog's suggestions are very good and you can hit all of them. Mystic, Watch hill, Newport are places you can spend a couple of days each.
2007 Hunter 49