I have measured the NYC Half course with David Katz several times (the NYRR has modified the layout almost yearly it seems. The first 6 miles is mostly within the traffic-free roads of Central Park; after that it's city streets, including Times Square and the West Side Speedway, er, Highway. Even though we measure late night/early morning NY is truly the City That Never Sleeps.
The first year we had an NYPD escort for the street section but subsequent rides we only had NYRR staff in an SUV equipped with a police package light setup (we were told "don't ask" when we inquired how they got that setup.
There's nothing quite like pissing off NYC drivers while you ride!
Incidentally one of the diciest parts of the ride for me is near the end going through the Battery Underpass tunnel at the lower tip of Manhattan. The safest I felt there was the year it was closed at night for repairs of flooding damage from Sandy. Truly an ill wind that blows no one good.