Season 1 is Seattle, actually, while 2 is Denver and 3 is New York. (4 was Seattle again, but not yet finished.)
Nothing Mission-wise for Boston yet.
Boston gets some info after Fuchi folds, when Novetech gets born. I'll have to poke around the books, see what's out there. It used to be the home of teh East Coast Stock Exchange, which moved there after the earthquake that levelled NYC, but after WInternight detonated an EMP-enhanced nuke near Boston, it moved back to the rebuilt New York Stock Exchange.