I usually take the train from where I am in the western suburbs of Boston to NYC.

But... doing so requires driving an hour in basically the wrong direction to the suburban Amtrak station. And then it takes longer than driving directly would. The only reason I do it is that I hate driving into Manhattan and parking there. Whereas when I arrive by train I can just walk to my hotel.

And, yeah, for Boston to DC I'll typically fly. The train is viable and I've done it but it's a full day trip vs. a short flight. And one of the airports is right on the metro vs. the NYC airports which are not.