Interesting. I couldn't discern the direction the trains were traveling as I couldn't see the trains from below and the sound was reverberating off buildings and the concrete piers of the viaduct above. I assumed is was a downshifting for a climbing grade but now that you mention it the trains could have already passed over the bridge and in reality what I was hearing was the application of the dynamics brakes on the downward grade (0.7%) on the Queens side, (Eastern Viaduct) as opposed to my perception that the trains were approaching the Hell Gate from Queens. There is also a curve, though slight, at the location of my house so the dynamic breaks may have been used to negotiation the curve as well as the downward grade.
There is more to this than meets the ear.