I read somewhere a while ago that the rental companies and legislature were looking to change the vicarious liability law that was behind the surcharges for NYC residents outside Manhattan and Staten Island.
Avis/Budget and National/Alamo did not have these surcharges. To the best of my knowledge, they don't have local offices in the outer boroughs, either, though. Enterprise didn't have the surcharges, and in fact does have neighborhood stores in those places. I read in that article that Avis knew of the higher risk, but didn't want to push away potential customers in an expensive market. Hertz and Dollar had been the ones with the surcharges. Dollar's surcharges were for NYC renters renting in Manhattan, JFK, LGA, EWR, and PHL. Hertz's surcharges were for NYC renters renting anywhere in the country.
Then the article said, Albany changed the law, with a compromise: CDW for rentals originating in NYS can be a maximum of $9/day, taxable of course. So Hertz now has on their website, "Rates now available to NYC residents," and the surchage paragraph has been removed. Dollar is the lone holdout.