Well, if you head to Greenport do me a favor and check out the Townsend Manor Inn Marina or Mitchell Park. Both are supposed to be good places to stay close to downtown. We're thinking about staying there for 3 nights later this summer and have never been.
Montauk is a nice stop but its not so convienent when it comes to downtown access, shopping and trips to the beach. I personnally like it because the marina is in a nice location with pool and square bar but the family was less than impressed last time we went....which, by the way, was when power went out in the entire north east....remember that? It was genset city at Montauk, quite a site everything pitch black accept all the boats running lights and TV's off the genny.
We're also stopping in West Hampton Beach for a few nights and never been there.
Hope you get some good recommendations. There's always Newport for you but that might be more than the 30nm limit.