You might stay on the same train at Penn Station, but it's anywhere from 15 to 45 minutes stoppage. Not the usual minute or two at an intermediate station.
From DC Union Station to Boston South Station, its about 6:45 on Acela. It's about 8:00 using the Northeast Regional. The Acela saves a decent amount of time between DC and NYC - about an hour - but maybe a half hour from NYC to Boston.
So yeah, seven to eight hours on bumpy train vs an hour on the plane are the options. Even having to deal with TSA and the airports in general, it's still half the time.