I am pressed for time today but I did want to quickly put out an overview of NJ TRANSIT trains.
RiverLINE - Bikes are allowed at all times, each rail car contains 3 vertical racks.
NE Corridor Line - Rush hour peak direction restrictions, new Comet V cars have tie downs for bicycles in the center vestibule.
Atlantic City Line - Bikes are allowed at all times if space is available. Use the wheelchair space which often has a special tie down rack (bungee cord is recommended, but your helmet chinstrap may work in a pinch)
Atlantic City and Ocean Drive - Atlantic City Station
Delaware and Raritan Canal - NE Corridor Hamilton and New Brunswick Stations
also RiverLINE Cass St Station (Locks 1 and 2)
RiverLINE runs along the new section of the D&R Canal south of Trenton