By the time you add airport parking and transport from the airport to the city (unless you take the subway) it's break-even on price for DC->NYC. It's easily break-even on timing given that front door to train in Union Station is 15 minutes, and, as you point out, you're dropped in the center of Manhattan.

DC->Boston full trip would obviously be insane - it's 6 1/2 hours even on Acela. But, probably preferable to driving.