Quite a few things were remarkably accurate, at least to my eyes. College Square is almost a dead ringer for Harvard Square, Trinity Plaza is more or less the same (though Trinity Tower isn't quite where it "should" be), and even Hubris Comics and Proust are close enough to their real-world equivalents that I could find them in-game without much trouble.
A lot of things are "off," but mostly due to scaling issues. To name a few, Boston Common, Faneuil Hall, and the Revere Plaza (where the statue of Paul Revere is) are all way too small. I didn't even recognize the Common for what it was until I saw the State House. Similarly, Concord is way too close to Cambridge, and the Science Center, while recognizable as the Boston Museum of Science, just isn't big enough to hold a T. Rex.
And some things are just plain different. The sprawling brick-and-concrete desert wasteland that is Government Center (I may be biased) was never built in the Fallout universe. Instead, you still have the remnants of Scollay Square in Goodneighbor, and in the tumble of buildings leading to Faneuil Hall. Kinda cool; I never really knew where Scollay was supposed to be until I played the game...
I haven't made it to South Boston or Quincy yet. I used to work in the one and live in the other, so they'll be interesting to see.