One additional reason is that a not insignificant amount of the funding comes from New York State. NYS and NYC are in a permanent love/hate relationship, and any process that concerns using tax funds originating from NYC to other parts of the state or vice versa is always difficult.
Except for our state-level income tax: NYS is very content to have NYC disproportionately pay into the state's coffers :-)
(Taxes don't bother me, mind you. What bothers me is that NYS treats NYC as a piggy bank while also keeping the city in a permanent financial chokehold.)