Wild idea I've had over the years, and never thought something like it would actually be proposed!
http://www.ny1.com/nyc/all-boroughs/politics/2017/05/12/storm-surge-barrier-calls-breezy-point-connect-sandy-hook-new-jersey.html(What I imagined was just a bridge-tunnel combo, like the ones in VA, and it would connect to Brooklyn or maybe both Brooklyn and Breezy Point. Perhaps like an extension of Ocean Pkwy.
Since they talk about putting a road on it, then NJT buses would run across to Stillwell terminal. Or, perhaps you could run a railroad over it, that would branch off the NJCL around Long Branch and have a terminal near the Ocean Pkwy station (Beach Walk, which is sort of like an alley, could perhaps be used. In the bridge-tunnel idea, it could be the entrance to the first tunnel).
Would this be a good alternative for some to the tunnels directly into Manhattan, and Penn Station and Port Authority?