I can find only two ways across the Hudson River - the tunnels into NYC's Penn Station and the bridge up in Albany/Renssalear. I know the Penn Station tracks connect to both the LIRR and the old West Side branch (Amtrak uses the latter for various services north out of New York and up the Hudson Valley), but I wasn't aware of the tunnels being used for freight... Anyway, just curious. Thanks
The Hudson River tunnels are exclusively passenger trains. All freight bound for New England goes up the west side of the Hudson on CSX's River Line to Selkirk, then eastward. Dieter Zakas former CSX conductor
To add to this, only electric engines are allowed in the Hudson River tunnels (meaning any freight traffic would need to go through two changes of engines), and the tunnels also have limited vertical clearance.