In Fallout 3 side quest "The Replicated Man", there was a connection to the Commonwealth Institute that's suppose to be similar to MIT. Players encounter a scientist named Dr. Zimmer who comes from The Commonwealth, a “war-ravaged quagmire of violence and despair” where he notes he and his colleagues created androids that have escaped and are running wild. Zimmer also references The Institute, which is presumably a future version of MIT.
The previous games took place in washington d.c., pittsburg, neveda, and maryland. Bethesda has declined to comment on the rumor of a Boston setting for now, but considering the impressive amount of mythology already revolving around The Commonwealth, it certainly seems like a plausible theory.
