OK, now we have at least three groups of people on this list who went through essentially the same: taking pictures => police called in => no, no, nothing illegal, but we were called, and we must respond.
As Auric Goldfinger once put it to James Bond, "Once is Happenstance. Twice is Coincidence. The third time it's Enemy action."
Note that your impression
The officer acted like he DID NOT want to be there.
exactly coincides with mine. Like I mentioned, in our case NJT cops were standing there speechless and all but demonstrating their lack of interest. The ones who ran the show were Bayonne cops; perhaps we were just "lucky" to come across one who's sighting a promotion...
I should also have stressed that we WERE standing on NJT property (but only publicly accessible parts thereof) while taking some of our pictures. However, this was never presented as an argument until the very end of the conversation, when The Plain-Clothes Guy did mention it (according to my friend - somehow I didn't really pay attention). However, the finale was actually the same (one more point left out of my original post): "If you guys want to do it again, obtain permission from NJT." - "Permission for what? For taking pictures from public property?.." - "Just get their permission, and you'll be fine."
Anyhow, the picture looks clear now. Obviously, it's perfectly legal to shoot from public property. It's doubtful whether it's legal to do so from NJT's property - New York and Boston representing the two known opposite practices. On top of that, however, we have the drivers/fare inspectors/supervisors who are under instructions to report photographers. Esp. "in our times", you can hardly prove your case against an instruction to call police if any suspicious activity is observed, and the boundaries of "suspicious activity" can stretch ad infinitum - while most of such activity of course remains legal. The rest depends, among other things, on the mood of the cops who happen to be on duty at that time; but one can suspect that if you laugh into their faces and say, "Look, I'm not doing anything illegal - say what you want, but I'm going on with my pictures; watch me if you have no other business", - a hitherto friendly conversation may turn into something more challenging. The choice (hopefully) is still yours.
(Actually, in our case - where we were actually cooperating - one of the cops did mention that they have the right to hold us for up to six hours without arresting or charging us, just for conducting an investigation. In fact, he wasn't quite confident; "I think it's six; don't quite remember, but something like that" were his words. Could we have caught on to this soft spot of his and started acting tough? Perhaps. Problem is, I suspect he'd be quick to find someone who WAS confident; what would the possible consequences be?)
That said, I maintain my viewpoint that (i) the practice of reporting photographers is idiotic, (not only, but in particular) because it is a wasted effort - the real bad guys being smarter than the authors of the idea would like to see them; (ii) in broader terms, a huge part of the current "anti-terrorist" policy is but a PR move. Unfortunately, the very reason the art of PR exists is that in general, it sells well. People tend to look at, and evaluate, the packaging but not the contents...