Assuming you've timed those yellow phases and you're not relying on perception (which we know is often off), report them to NYCDOT before they cause any more damage than they already have.
As I said, all the yellow phases that I've timed in NYC are 3 seconds long, on major and minor streets alike, all with speed limits of 30 mph.
I see cars run red lights every day. Usually it's the obvious result of impatience, or of pushing a yellow a bit too far. Occasionally when I'm driving, I'll slow down to stop for a fresh red and the car behind me will pull into the other lane, speed up, pass me, and run the red light. I don't think I've ever seen such a driver get a ticket for running the red light. If only the intersections where this is common had cameras!
One of the factors used to determine yellow phase length is the speed limit, but it's not the only one. And based on the information you've given, it's impossible to tell whether 3 seconds or 4 seconds is more appropriate at the intersection in question even if the speed limit were the only factor. Perhaps it was determined that 4 seconds was too long at those locations. (Or perhaps not. I don't have enough information to go on.)