Pour Judgement on Broadway is my place of choice in town. Coddington Brewpub in Middletown is pretty decent too. That's pretty much it in my opinion for good craft. That said, there are no shortage of bars on Thames street. Cheers.
Pour Judgment & Yesterday's/the Place are your 2 best bets. PJ is a bit on the small side, while some have had issues with service & stale beer @ YtP (I haven't though). http://beeradvocate.com/beer/profile/4562 http://beeradvocate.com/beer/profile/15775
Pour Judgment is the place you want. Yesterday's is like a time warp - I mean the trivial pursuit cards on the bar are from about 1985. But you can get a decent beer there. Buskers Irish Pub on Thames isn't terrible - 20oz pints and a decent atmosphere with a few beers I wouldn't kick out of bed. The Pier used to be a decent spot, with a nice outdoor bar serving Delirium and a few others. They were having some weird liquor license issues when I was there last month though so the outdoor bar wasn't even open.