the big question is where in Boston will you be staying.
The good part is that most of these places will be accessible from The T (MBTA; public transportation) For the Cambridge area, Lord Hobo, Cambridge Brewing Company and Meadhall are all less than 5 minute walk.
IN Brookline I would recommend the Publick House. Sunset in Allston/Brighton.
For breweries, the big guys like Sam Adams and Harpoon are worth a visit, the little guys like Trillium, Mystic, Nightshift and Idle Hands are worth the trip.
If you are driving in, Jack's Abby in Framingham (about a half hour west) is absolutely worth the trip.
For bottle shops, The biggest and IMO best is about another half hour from Jacks Abby, Julios Liquors in Westboro. Huge beer selection with tons of locals and foreign.
You probably already know about Yankee in Attleboro.