It would be in yurup.

Most obvious infrastructure and military targets are packed into a very dense area in central Europe. One of the main reasons why I dont want a DLC taking place in Europe.

Boston would have been a target because its a large population center

Being a population center doesn't necessarily factor in why it would be a target. Its a state capital therefore a major target because of its leadership role. Its also a major seaport and technological center which would help the US in its war effort against its enemies.

And communications center.

The population would just be icing on the cake.

They are a fairly important city, trade wise (though provably not as much so with a locked down US), with a naval yard and a lot of historic value. I'm guessing it would be hit fairly hard.

The color. Boston had ,or has had a LOT of printing presses. Perhaps there is a surplus of dye or raw pigment?

It makes sense Boston would be hit hard, because of the symbolism it has. The American revolution was based out of Boston with the tea destroying revolt and would be seen as the birthplace of the USA.

If the trailer is anything to go by, the prewar scenes show at least one fairly massive atomic bomb going off in Boston. Though this could be explained away as a Vault's over exaggerated dramatization of what happened.