Suburban interests are usually not aligned with the needs of an urban environment, and smaller administrative units always resist and win against consolidation efforts. Everything from patronage, NIMBY, well-run local governments to outright racism are factors. For residents, it's typically easier to deal with a village or town hall type entity than trying to navigate the bureaucracy of NYC municipal government.
Maintaining things like school districts, towns, villages and special districts will always be local priorities that always win against regional initiatives. You probably have 50 police departments alone just on Long Island, with at least 50 collective bargaining agreements that would need to be consolidated and dealt with. That's 50 police chiefs who need jobs, and thousands of generously paid policemen who would need to integrate with a larger and less generously paid NYPD. You'd have the same situation with school districts.
The formation of "Greater New York" (New York City) was only possible in the 1890s because the political machinery was in place to allow annexation and takeover to be effective. Tammany Hall was more powerful than the opposition. State administrations in New York have been trying to encourage consolidation and shared services for decades with very limited success. Even dying places in Upstate New York want to hold on to local autonomy.
