Absolutely nix on Seaport Marine. Holds the prizes for both the worst and most expensive marina I have ever stayed at. Unless they have done huge upgrades in the last two years (physical plant and personel) , avoid at all costs. Their only plus is proximity to town; but why not just stay at the Seaport itself if that's what you want?
Also +1 on Brewer"s Branford. Haven't taken my own boat there but visited a freind. My advice is go check all these places out first by car if you are a local. Since you like the Thimbles, for another fun non-marina site, try Hamburg Cove off the CT River. All moorings, very pretty and fun, especially if you have a dinghy.
George
Hatteras 56MY
Boston Whaler 130 Sport