The Federal Air Marshall's Service is part of the Transportation Security Administration (TSA). The TSA is not only responsible for airports, but other modes of transportation to include rail, bus, etc.
Here is a link to what they do:
TSA | Transportation Security Administration | What We Do
One thing specific that comes to mind is the new Transportaiton Worker Identification Credential or TWIC card that anyone accessing the Ports must have. This requires a background investigation to include checks of criminal history, terrorist watch lists, etc. Compared to the Sealink card that Port Authority issues, this is a higher level of security for our Ports.
And yes, FAM's do ride on trains even though they are called "Air" Marshalls as part of their job duties. That doesn't mean there are less of them in the sky. Most federal agents, even on vacation, are actually encouraged and fly armed on commerical flights. When that happens, they can move the FAM to cover another flight, train, etc.