Nobelist William Vickrey famously wrote about congestion pricing and thought that entry and exit to and from Manhattan would be a good place to try it. Almost 40 years later, a version of the idea for Manhattan was proposed and defeated. The New York State legislature balked.
Ken Orski reports that: "What emerged from our conversations with opponents as well as advocates of the plan, including several state legislators from both parties, is a complicated tale of a bungled strategy to steer a complex and politically vulnerable proposal, in an election year, through an alienated state legislature that was predisposed to treat the mayor’s initiative with skepticism." Politics is very difficult.
He also writes (Innovation Brief. April 10, 2008; not yet online, as far as I could tell) that outer-borough auto commuters to Manhattan thought they would bear the costs while the funds would be used to improve transit service within Manhattan. Here I have to mention again that Don Shoup and his colleagues ("The political calculus of congestion pricing") have stressed that any pricing revenues must be carefully directed so as to assemble a winning political coalition. They suggest, for example, that communities traversed (and perhaps injured) by freeways be supported first.
The legacy of Robert Moses is that New York has plenty of such neighborhoods. That would have been a place to start.