I know a great transmission shop in Methuen (about 20 minutes North of Boston). Its actually called Methuen Transmission. The shop is owned and run by 1 guy, and he's pretty damn good. You've never seen such a clean shop in your life. Since there is only one guy there, you know he's the one working on your car/tranny.
However, if you're looking to keep it economical, this isn't the place for you. He's good, and you pay accordingly. He doesn't rip you off, but he's not cheap either. Service is top notch though.