Just to clear up a lot of the misleading spin - NYC was never handing Amazon $3 billion. It was tax abatement, which simply means instead of getting all the free money, NY would only get a portion of free money.
Like if I told you I was going to give you $100 and you said "no, no, $70 is fine". You are not giving me $30, you are getting a free $70 instead of a free $100. Now there's a free $0.
Further, NYC is not Manhattan. The outer boroughs are underdeveloped - there is plenty of land to build housing, especially if built vertically. Public transportation is overtaxed - but that's due to NY's own mismanagement, not because there's some natural law that says public transportation is at some physical limit.
A reason for the underdevelopment of the outer boroughs is the the lack of subway lines that serve them. This could've been an opportunity to change that. The NYC economy is overly reliant on finance, as the great recession showed, and it seems that will continue.
There are legitimate questions about gentrification and how long time residents would've been affected. But it is revealing when someone thinks driving away job creation and economic diversification to stick to a status quo that isn't so great to begin with is a "victory".