You all are losing historical knowledge here.
Before Amtrak, the PRR went all the way to the Jersey shore, and then ferry shuttled passengers into NYC... and it was FREAKIN' SLOW
in comparison to today. You had to detrain, walk to the ferry, get ON the ferry, sail across the Hudson, get OFF the ferry, and then walk to the subway. PRR had the insight to actually get a tunnel built in the first place to cut out all that crap and get folks into NYC's Manhattan as fast as possible, and then another out to Long Island.
And now you want to go back to ferries? Something that'll add an extra hour and likely will not have the capacity to haul even a full Northeast Regional over the Hudson in a timely manner (even with extra boats)?
Granted even the PATH train can handle some of the load but not all of it -- NJ Transit had to redirect traffic to Hoboken and get folks on PATH and a ton of extra ferries, and even then it wasn't enough!
We killed that ferry idea back in 1910. Howard Tayler was right. Every few generations, the really really bad ideas come around for another go.