I am not aware of any information to explain why there isn't that much damage to Boston itself.
But Washington DC (Fallout 3) should have looked like the Glowing Sea in Fallout 4 or worse given that it is the capital of the United States and therefore the number one target.
To explain Fallout 4 and Fallout 3's main cities being remarkably intact we can go with developer comments on Fallout 3. Paraphrasing: "playing in a completely destroyed city wouldn't be fun."
Still that being said the Boston Area shows signs of rebuilding, possibly by the institute at some point in the past. The people in the commonwealth themselves have a better degree at rebuilding than those in the DC area.
We also know from Fallout 1 and now Fallout 4 that the enemies of America put more emphasis on destroying locations associated with research rather then cities. Area's with research that clearly aren't destroyed as badly as the Glow and the Glowing Sea might have not been known to the enemies of America and or were classified as civilian and therefore low priority.
But yeah the cities should be far more destroyed then they appear to us, but it wouldn't be as "fun" if you couldn't recognize the city you are playing in. After all we all know full well what a single nuclear bomb can do to a city let alone dozens or hundreds.