The flags at Faneuil Hall are historic ones, so you'll be able to buy a Grand Union, Bunker Hill, Charlestown, and Don't Tread on Me flags. These are the same flags you can get at the Charlestown Navy Yard Visitor Center. I believe you can get some 1812 era flags at the USS Constitution Museum. There aren't really places to buy a MA flag or city flag anywhere downtown, would be easier to order it online probably.