From what we've seen of the BoS, I'm confused on which branch they're from? I doubt they're another western chapter sent on an expedition, since it seems by now the western BoS is in no shape to be doing more expeditions even if they wanted to. Maybe it could be Lyons' chapter, but if the game is set during or shortly after Fallout 3, I don't think the CWBoS is any shape to be in Boston when they barely have the power to hold out in DC.
So I'm guessing judging by the vertibirds and airship, the BoS in Boston are either from the Midwest, or if the game is set around 5 to 10 years after Fallout 3, maybe it's Lyons' group that managed to somehow build an airship and got a bunch of vertibirds from Adams Base. (And basically much stronger than what they were in 2277) What do you guys think?