I know that Philadelphia has a subway system. IIRC, basically a north/south run on Broad Street and an east/west line on Market Street. Again, IIRC, Market Street line is both underground and above ground.
http://subway.umka.org/map-philadelphia.html
I do not remember any mention of flooding on the North/South line. I used to use it to get to Temple University. While I went to Temple, the subways were a relatively safe and effective way to travel. The two years I went to Temple, I never had any problems.
With T2k both V1 and V2.2, Philly gets nuked pretty hard because of massive oil refineries in South Philly. I could see maybe the north end of the subway down to say City Hall MIGHT still exist....Could be a lead in for scavenging the Temple Library as an example of a scenario..
My $0.02
Mike