The best brewpub in the Boston area is probably the Cambridge Brewing Company, with a long row of GABF awards hanging over the bar. It’s just over the river in Cambridge and easy to get to by public transportation (Red Line to Kendall Square/MIT). In the neighborhood are some great beer bars, including Lord Hobo (which usually has a few really distinctive beers on their 28 taps) and Meadhall (with 100 well maintained taps). In Boston proper (and up in Salem) are scattered a few Boston Beer Works brewpubs, which usually have a large selection of solid beers and occasionally something particularly worthwhile.
North of Boston, I agree (highly) with the recommendation of the Portsmouth Brewery pub. Also, The Tap, in Haverhill Mass. is an excellent brewpub. If you are here between November 10-12, The Tap will be hosting the annual NERAX North cask ale festival, with ~40 casks of real ale split about evenly between New England and British breweries.
If you want to take a big brewery tour, I like the Harpoon Brewery tour, but a lot of people like the Sam Adams tour in Jamaica Plain, where they make their small batch beers in the 19th century Haffenreffer Brewery building.