I agree with the previous posts. If you are short in time, definitely see the World Trade Center and the PATH platforms. From the street, one can see the "box" through which the #1 West Side train runs (South Ferry to 242nd Street). Unless there is a weekend service interruption when you visit, a trip to 242 street Van Cortland Park, with getting off the train at 125th and 207th northbound, waiting for the next train, is worth the excursion to New York and is economical in time. Because of the cursed full-width cabs, one has to get onto a station platform to get a good view of the tracks.
See #1 schedule at
www.mta.info for trip time. Exploring NY subways can be very time-consuming for a railfan tourist, so plan ahead. You also ought to see what life under the el is like, and for that I urge a trip on #7 and a walk from 61st Street (Woodside, Queens) outbound towards Junction Blvd. No wonder NY is a cosmopolitan city!
I also rate the J highly, westbound, with a railfan window on most trips. Now, that raises an interesting topic: Where will a railfan tourist find clear front windows: on PATH to New Jersey (Newark, especially), on no numbered route (am I correct?), on the E and J. Others with a guaranteed view?