Yeah, the MARC train would only take you to Bowie, I think, and that's probably the closest you'll get using public transportation. The area is served well if you need to get to the immediate DC suburbs, or between DC and Baltimore. Anything west or east of that immediate corridor and you're on your own.
I was just in Baltimore a few weeks ago, and used the Light Rail and MARC train to get from my hotel in Baltimore to my next hotel in DC. I had never realized (or maybe just never checked) just how close they are. Took about 45 min or so to go from Baltimore to DC.
No idea about record stores in DC, although I did see a FYE in Union Station!