A few convenient Zipcar and rental spots on the east coast I know from experience as a frequent train rider who occasionally needs a car:
-In NJ, there are cars at MET and PJC, though they sell out often. (And I think the MET one is listed as "NY Metro-NJT" or something obscure like that.)
-It's really only useful for NJT riders, but there's an Avis office at the New Brunswick Hyatt, two blocks from NBK, that I've used before.
-In northern Virginia, a bunch of Zipcars are available at the King Street metro stop (adjacent to Amtrak ALX) and Braddock Road (one stop down, less than a mile away) as well as Franconia-Springfield (Metro terminus, former limited Amtrak stop, still a VRE stop).
One cost-saving tip is that if no one has booked the car right before you, you can get in the car 15 minutes early, no extra charge. I'll often try that both to save money and to get familiar with lights, mirrors, etc.