Although the 25 minute transfer times is a bit tight if your NJT is late, if it's not, you're quite probably fine. Not sure why you would want to board your Amtrak train through Moynihan, nor why you would want to go there at all on this trip (except sightseeing or novelty). You can board the Pennsylvanian in Penn Station. There are boarding gates in Penn Station as there have always been. NJT is also in Penn Station. To reach Amtrak, you exit NJT, make a left turn in the corridor, and walk directly into Amtrak. The boarding gates are beyond the seating area. Amtrak usually boards 10-15 minutes prior to departure. So IF (I say IF) your NJT train arrives relatively on time, you have about 10-15 minutes to reach the Amtrak gate -- which should be enough if you don't dally. They'll probably be boarding by the time you reach the gate -- if the Pennsylvanian is on-time. There are monitors to show you your Amtrak departure gate, once it's posted (usually 10-15 minutes before scheduled departure time).
People might not realize that Penn Station and Moynihan Hall are in separate buildings, and importantly, Moynihan Hall CANNOT be reached directly from Penn Station. You have to EXIT Penn Station, CROSS EIGHTH AVENUE on the street, and then enter Moynihan Hall. (If Amtrak plans to remedy this by building a corridor or tunnel from Penn Station to access MH in the future, great). Hence as things now stand, with just 25 minutes for your transfer at most, you should forget Moynihan and stay in Penn Sta.