Your choices for running routes in New York are limited only by your imagination. In Manhattan, the obvious choice is Central Park: roads there are closed to traffic on mornings, evenings, and weekends, and the perimeter route is more than six miles long. You can also veer off the pavement and take the 1.5-mile loop around the reservoir and through the adjoining dirt bridle paths. Outside of New York's biggest greenspace, my favorite run in the Big Apple is along the Hudson River in Riverside park on the Upper West Side. Outside of Manhattan, check out Prospect Park in Brooklyn, and surprisingly serene Van Cortlandt Park in the Bronx.
You can find a running map of New York here.