Some parts of the NY metro area need floodwalls; I can't think of another way to protect lower Manhattan, or the infrastructure around Penn Station NY or Sunnyside Yard, and those are not reasonably relocatable.
But several of the less-highrise-filled sections of the metro area should be cleared of permanent residents. The various barrier islands need to be allowed to *do their job* as barrier islands, which means not filling them with housing and roads, and keeping people on the land *behind* the barrier islands. This applies to the Rockaways, the islands south of Long Island, and the barrier islands of New Jersey. Within New York City, the areas of the Gowanus Canal and Newtown Creek should be re-naturalized to absorb water.
Hoboken Terminal is an implausible object to start with. It's built on short pilings for goodness sakes! Even though it's an entertaining historic building, it should probably be shut down and replaced with something on higher ground. It made sense when it was dumping people onto ferries, but that isn't the primary use any more. There's been too much construction in flood plains. It needs to stop.
The problem of the rail lines between the Palisades and the far side of the Passaic River is a difficult one. That area gets flooded from the ocean and from the rivers, and is subject to high winds during storms as well. It's hard to see a reasonable route even if you go quite far north or south.
One thing is clear: the Harlem Line needs to be reconnected along high ground to the B&A (whether it follows the old Harlem Line route, or perhaps a new, fast, direct route); having all of the routes out of Manhattan be floodprone is simply not a good idea.