Lower Manhattan reference, not every borough's skyline
Times are computed for the New York City reference point in Lower Manhattan at 40.71° N, 74.01° W, with a flat horizon. Across the five boroughs the difference is about a minute, but buildings are not: in Midtown a rising Moon can stay hidden behind towers for a long time after moonrise. The East River, the Hudson waterfront and Brooklyn and Queens shorelines give the lowest open views to the east, where the Moon rises.
Source: GeoNames — New York City