DAVID J. CAROL
For all photographers living in NYC or visiting, here is the rule about taking pictures in the subways:
Restricted areas and activities.
3. Photography, filming or video recording in any facility or conveyance is permitted except that ancillary equipment such as lights, reflectors or tripods may not be used. Members of the press holding valid identification issued by the New York City Police Department are hereby authorized to use necessary ancillary equipment. All photographic activity must be conducted in accordance with the provisions of this Part.
MTA NYC - Rules of Conduct
My understanding is that the MTA's concerns with lights and flash is that it could distract or temporarily blind the train conductors while they are arriving in the stations. As far as tripods go, they could be an obstruction to passengers and someone could stumble over them. I also think there is a concern that a tripod and camera might get knocked over into the tracks or into a commuter. Be safe, be polite and go take pictures. The subways are a fascinating and inspiring environment to photograph. Have fun folks!