Ongoing climate change is both going to make severe storms like Hurricane Sandy more common and also raise baseline sea levels and increase general risk of coastal flooding. We're seeing today that even when loss of life is fairly minimal, the indirect economic damage of flooding a major urban area can be severe—power will be out in New York for days, and nobody really knows when the subway will be back up and running. Unless the city can reasonably safeguard itself against flood, the consequences are going to be disastrous. We can—and should—hope for global action to reduce greenhouse gas emissions but it's extraordinarily unlikely that as much will be done fast enough to prevent the need for substantial adaptation measures. That's particularly true for a densely populated wealthy area like Greater New York City where even fantastically costly investments pay off if they're needed to avoid rendering the massive amount of fixed infrastructure already in play useless.
The best place to look for guidance is probably the city's former colonial overlords in the Netherlands who've been trying for a while now to market their flood control expertise through their Holland Trade website:
Climate change, expanding economies, and urbanisation are putting the world’s delta populations at risk. Dutch expertise is at hand, however, in the form of hydraulic engineering, flood control, flood protection, foundation technology and infrastructure. The Dutch are renowned for their ability to design and build storm surge barriers and levees, reclaim land through high-tech dredging and engineer entire coastal areas and harbours. The Dutch also excel at river engineering and maintenance and are pioneering climate adaptive construction, which allows houses to be built in flood-prone areas.
The idea of essentially damming up New York Harbor sounds extreme, but that's equivalent to what the Dutch did with the Zuiderzee Works and especially the Delta Works projects undertaken after the 1953 flood. Some of the Dutch works are permanent dikes, but others are open sluices that merely shut when storms are coming to block surges. The idea is to in effect shorten your coastline which makes it easier to defend with high walls.
You could imagine something similar at the Arthur Kill and across the Verazano Narrows or even between Sandy Hook and Rockaway. Projects like that wouldn't immunize Staten Island or the beachfront parts of Brooklyn and Queens from storm surges but they would defend Lower Manhattan, the badly flooded Red Hook part of Brooklyn, Long Island City, LaGuardia Airport, and a big swathe of New Jersey.