Well, Hunts Point Terminal Market is a big user of rail, with covered hoppers, insulated boxcars, and mech-refs. There is a road curving south west from the Terminal Market, which is parallel by a branch which once served several large modern (1960s or later) food distribution facilities (we have discussed this on this board before, along with much else that I will mention).
Heading West you come to Oak Point, west of the Bruckner, which usually has much interesting rolling stock - there are a few industries rail served in this area, including the NYCTA which (I think) takes covered hoppers off Barry Street (a block further south is a short section of Elevated used for training purposes).
Even further south is Port Morris, with both the existing M-N section of the Northeast Corridor, and rememants of a fairly extensive grade level branch system (also discussed in depth on this board a year or so back - you have to hunt but the rows are still visible here and there). Curving west into the former Harlem River Yards, there is an operational waste transfer operation there, and I think the NY Post (wonder if they are still receiving rail at their fairly new plant there). Don't forget the funky oval freight house the CNJ had on the Harlem river east of Third Avenue - served by car float.
Following the Harlem River up, past the Bronx Terminal Market (which once had a simple switch back track arrangement, currently serves as a ethnic wholesale food mart, and which the city plans to turn into yet another shopping strip mall, you arrive at two industries in Riverdale/Kingsbridge which I often observed in my time in the Bronx (mid-1980s) - Stella D'oro, on the old Put around 236th (I think) and Broadway - they recieved covered hoppers, and probably still would if ConRail wasn't run by a bunch of stiffs (as to Stella D'oro I still remember that great aroma in the mornings), and also around 230rd St and Corlear was a fairly large U-Haul storage place, usually had 2 - 3box cars at the loading docs (which you could look down on from 2 stories up from Corlear/W Terrace) - the spur snaked past Kennedy High School to the east of the access road. Now, I thought this was fairly interesting (from the perspective of a college student growing up during the black days of the '70s, on fairly freightless Long Island, it was), but about a year ago on the NY Central forum, I learned from some knowledgable old-schoolers that the area between Marble Hill, 230rd, and the winding Johnson Ave was a full-fledge NYC freight yard, complete with auto-unloading ramps (and even better, RMC had an article around that time detailing the AMC auto-loading facility in Wisconsin, complete with pictures of the flats and trilevels which shipped their automobiles East to NY - yep, to be unloaded in that very yard). Damn, when I got to visit all that was left was the U-Haul spur, Kennedy High School (built I guess in the early 1970s), and lots of empty ground (which I think a EMS/Fire house was eventually built in the 1990s). There of course was much, much more (for instance, by Oak Point yard, on the East side Barry St, there was a funky looking factory which had a 2 slot siding crossing Barry St and all enclosed by Chain link fence - when I first saw this in the 1990s it had a boxcar - when I finally got back to visit, I never saw a freight car again).
I recommend scanning the NYC, the PC, the New York State forums, going back as far as possible - you never know what you may find.