I'm looking for Boston-area breweries (not Sam, not Harpoon!) which, in addition to selling draft in their pubs, also bottle and distribute from the bar or in a local store. That is to say -- is there locally brewed beer I can enjoy at home?
I know you can buy growlers from the ones that people listed. Another one to add is Beer Works. I like their beer too.
go for the Cambridge Brewing Co - available at their spot or some of the better beer bars around town - it is considered a higher quality craft brew than some of the other local breweries, I would agree.
Many of the local breweries have wide distribution in local package stores, and give brewery tours (and tastings). They are also on draft in many local bars.
Harpoon (on the South Boston Waterfront) immediately springs to mind - and their tours include tastings.
So there are many pubs that can answer your question, based on what they sell. It didn't sound like you were interested only in brewpubs.
You should look into some of the "local" NH, ME, and VT breweries, as well. Lots of good microbreweries in New England:
There's a decent book out now that lists most NE microbreweries, with additional info such as their main brew and seaasonals they offer.
Pick up one of the local beer/brewing papers next time you're out for a beer (at Publick House, John Harvards, Bukowski's, Sunset Grill) they'll list all the New England microbreweries and brewpubs. Yankee Brew News has a particularly good set of maps showing locations in all the NE states. Burlington VT and Portland ME are pretty good choices for beer oriented weekend road trips.