If the Earle railroad was to be used for any sort of non-military use, it seems commercial use of the piers is out of the question then. Maybe you could use it to have a train running to the SeaStreak Ferry... not sure how many people use that ferry, and not sure how many people would use a MOM line that doesn't go straight to NYC/North Jersey, but requires you to hop off and get onto a ferry into the city. Not only would you have to improve the tracks from Toms River - Farmingdale to at least Class 3, but you'd also have to re-double track the Earle railroad most likely, and would need significant money to upgrade the ferry terminals in Atlantic Highlands.
Honestly, at that rate, you might as well just tear up the Henry Hudson Bike Trail, make it a railroad to the ferry again, and run a shuttle out of Matawan that would take people to and from the ferry terminal. And then have MOM originating in Lakehurst or Toms River, connect onto the Coastline at Red Bank (so people could transfer off if they want to take a train to NY instead of a ferry), and then terminate at the ferry.