Trainlogic.net is a site for train, light rail and subway schedules throughout the US. They have recently released an app for their services which lets you plan rail trips with up to two connections. The app also works in offline mode.
The app will also combine rail networks such as NJT, PATH, LIRR and Amtrak, if you want. It shows maps of your trip, any stop, and lets find out if the train you’re on is making it on time. The app advises you on peak trains, suboptimal trains, etc.