Pre-Acela and the electrification of the line north of New Haven that came with it, the only real reason you'd take the train from Boston to NY (much less points south) was to save money. When I was in school in the Boston area, when I went home to the Philadelphia area, I'd take the train for longer vacations but would fly for 4-day weekends.
Arriving at Penn Station has benefits if you're traveling for business. Hailing a ride to get to an office within 15 minutes beats the long ride to get downtown from one of the NYC airports.
Yeah, none of the NYC airports are particularly convenient. And I'm actually usually in midtown, often on the west side, so I can just walk from Penn to my hotel. (And Penn may actually stop being its dingy self one of these days.)
> (And Penn may actually stop being its dingy self one of these days.)
That's kind of already happened. The Moynihan Train Hall just opened up recently. I checked it out recently and it's quite nice, certainly much nicer than the old Penn Station. The next time you're getting off in NYC, walk towards the back of the train you came in on and then go up to the surface, and you'll be exiting in Moynihan instead of Penn.
I haven't been in NYC for close to a couple years at this point. Some of the renovation work around the LIRR entrances was done but not anything else. I'll definitely check out next time I'm there. The drawings for the continuing renovation look quite nice too.