Interesting that they'll consider DMU but took freight/passenger right off the table.
I thought the best way to get capacity would be to build a twin-bore freight/passenger tunnel from St. George to Brooklyn 65th Street, and 2 more bores for SIRT, then build double-track across the old North Shore for LIRR/Amtrak/NYA. I guesstimated the whole project at around $7-10B, but for a double-track freight/passenger route it would probably be around $250M less to use the North Shore than to tunnel all the way to Greenville. I figured each bore is about $170M per mile, and that the North Shore route is about a mile less tunnel, but still $100M to build a double-track line along its 5-mile route.
Since Arthur Kill is only a single-track bridge, you could probably save some $$$ by reducing the amount of double-track--but I would still think a double-track tunnel would be needed. In total I'd guess 5 bores: 2 rail, 2 transit, 1 maintenance.
Seems like it would be nice to have a Superliner- and Q-car capable route that goes from Jersey to Connecticut via SI, Brooklyn, and Queens, but local Congressional support seems to want to exclude it. I also thought you'd get more political momentum tying commuter, freight, and subway all into one mega-project. That way, it clearly benefits NYC and NYS, where the Gateway project is always viewed as a NJ requirement.