People always think of Sam Adams (sometimes unfavorably) when they think of Boston, but in reality, Boston is a wonderful beer city home to underrated gems like Harpoon (SO much more than Harpoon IPA), Pretty Things (amazing), John Harvard, Boston Beer Works, Cambridge Brewing Company, etc...not to mention dozens of amazing beer bars like the Publick House and Sunset Grill and Tap...in addition to the fact that it's hard to find a bar anywhere in the city that doesn't have at least one great beer on tap.
Asheville, NC is another new favorite of mine. Amazing beer city with tons of great options including but not limited to Highland and French Broad.
Need to make a pilgrimage to Portland soon.