Funny you mention Boston, as I'm envisoning that as a kind of 'end game' or a 'light at the end of the tunnel' for this campaign. I've decided to set the starting enclave in the 'town' of
Shelburne Falls. I live in Mass, but south of Boston, and don't really know too much about anything past Worcester, but I basically said 'what is almost in the middle of this state' and then I zoomed in on the Google map. Funny how those things work.
I also think it's a good setup because they have the Deerfield River which they could (cautiously) travel on, and they are close to Greenfield and the urban sprawl that carries all the way down to Connecticut and that coast. There is also a large amount of dams on the Deerfield River, so I imagine small groups have gathered along its banks to tap in to even 50% of the original output, which could set you up real nice.
I've also been pondering how the MilGov/CivGov '2nd American Civil War' might've evolved or de-evolved in the past 17 years. I guess it depends on if you follow the modules relating to their actions, and I guess you could say that someone got around to kidnapping the New America leader and investigating the Airlords, so New America probably isn't a threat. Unless some eager jump-start found a few booklets...
I can see small pockets of 'Pro-Military' and 'Pro-Civilian' enclaves in some states, but probably not as much in New England. Could be an interesting choice for the PCs and their enclave. Produce facts showing both sides aren't so hot, and they have to choose the lesser of two evils!