Permits are handled almost exclusively at the municipal level by cities, towns, and villages. The county provides planning oversight and regional coordination, but does not issue building permits for private residential or commercial construction. Specific flood zone reviews may involve county-level coordination for projects near major waterways.
How this fits with the state
The state authority here is Local licensing authorities; NYC DCWP / DOB in New York City. The county file does not replace that — it adds the permit office, local overlays, and the actual filing path.