It is my understanding that the Long Island Rail Road access will be East-West, connecting with several North-South subway lines in Manhattan - Grand Central Terminal. Lots of escalators.

New York Central's local service was built "under-running", while Pennsy's Local service on the Island is "top-running".

There is a freight line from the Hudson River line to the North approach to Hell's Gate Bridge.
TRAINS' Long Island freight service article. See TRAINS article on NEC freight service.

A track connection at GCT would be "interesting".

With the minimization of service to Albany, station capacity at GCT is reportedly available.

Between Long Island, New Jersey Transit, and AMTRAK all serving Penn Station, it is finely turned to near maximum. Fun to watch the West throat from above, during evening rush.

I believe Metro North is serving Penn Station via a surface freight line on the West side of Manhattan - diesel powered? - comments expected.

Thus, a lot more than trackage rights would be necessary - in my opinion.