FWIW, my son and I spent four days in the tri-state area last week photographing trains on every rail system except PATH. The only encounter we had was at Babylon on the LIRR when a local police officer drove up to where we were standing after we photographed a train of M-7's from street level and asked what we were doing. We explained that we were rail buffs and he said that was Ok, that he just had to check since there was heightened security after the OBL killing. We had no issues at all on the subway, although we probably didn't spend more than 15 or 20 minutes at any one station.
As information:
An acquaintance of mine is a subway operator (and railfan) in NYC. He has informed me (and other railfans we both know) that as of last week, all subway crews are to immediately call in ANYBODY seen taking photos of any kind in the subways to police. It's apparently the MTA's reaction to the Iowa switch-tampering incident.