Answer to your question
As of now, NJ Transit trains do not go directly from AC to NYC. However, somehow they are planning on accomplishing this miracle in the future. The scan-nj website (which is down right now) had a really good frequency lay-out for the NJ Transit Train system. I never used my scanner on the AC - Philly Train Line, however the last info I saw posted was that their operations frequency is 161.400. However, I have confirmed the NorthEast Corrider Line (from NYC to Trenton) uses 161.010. I would also always have all THREE NJ Transit PD frequencies programmed into your scanner as follows:
160.830 - Ch. 1 (main channel)
161.190 - Ch. 2 (used many times in larger stations)
161.370 - Ch. 3 (used many times in larger stations)