I think the sticking point is if/when the cross harbor tunnel is built, that would increase freight train movements (which is a good thing, less truck on nyc highways and the LIE). There's semi-opposing/competing interests on that trackage. Dangerous cargo would be banned from the tunnel, but it could take almost every other type of cargo that crosses over the river via truck. Perhaps the movements can be restricted still be restricted to over night, but from a transit perspective, it would leave people stranded at night. Would there be a bus replacement t night?