The thing about NYC that may not be quite familiar to people from other US cities is that mass transit is pretty good. It may be the case in SF that if you want to work in SoMa your choices are living in SF proper or spending at least an hour to get to work with a large standard deviation, but in NYC you can live in Astoria (Queens) work in Midtown (Manhattan) and have a twenty-five minute pretty reliable commute.

So choosing to live in Manhattan is a luxury rather than a necessity for most people. That's one reason why I think keeping affordable apartments in Manhattan isn't the right thing to be optimizing for (though it may well be part of a larger picture).