Well, I'm from CT & this is only my opinion. I know there's only a few cruise lines that go out of NYC; Norwegian, RCI, I think Princess(?) does or will and of course the QEII group. I'm sure I'm probably missing one or two.
The piers aren't that many, the one in NYC over on the West Side is still a disaster. That's the city's fault for not moving with the times. But with 9/11, the least thing on the city's mind was a cruise ship terminal. The mayor before Juliani was a joke & didn't care at all about a cruise ship coming to NYC. Back in the day, the most concern while Juliani was in office was cleaning up Times Square & knocking down the crime & corruption that was rampant in the city. Those that remember what Times Square was like before the cleanup know what I mean. Then 9/11 came & the concern was cleanup & rebuilding a piece of billion dollar real estate. Again, cruise ships? Who cared during those dark days?
The other problem is that, well, its darn cold up here! The winters here are brutul at times especially when you have a Artic Clipper. So since most of the East Coast goes into winter & the jet stream can knock it down to FL, well, you really can't stand outside on the deck. It probably would not start warming up until you go past the Carolina's. So why waste 2 days on a ship staying indoors? Plus the location on the West Side (I can't speak for Brooklyn site) there on the river does freeze up during the winter. So you need ice breakers to come through & break it up to avoid having ship hulls getting cut up.
Plus, you'd have to pack 2 sets of clothes - summer stuff & winter stuff for coming/going back to NY.
Beyond that? You'd have to ask the cruise lines. The cruises take longer going out of NYC, so you'd have a 7 or 9 day cruise, but not alot of islands to visit & lots of sea days.
My guess anyway.