New York Governor Andrew Cuomo said the 54-storey office building close to Times Square shook from the impact.
Governor Cuomo said the crash sparked a rooftop fire, which was brought under control. Some were evacuated from the tower, but none were hurt.
He said New Yorkers have "a level of PTSD from 9/11" when they hear news of an aircraft crash in Manhattan.
The pilot has been named by local media as Tim McCormack.
He was the only person aboard the Agusta A109E helicopter, said the Federal Aviation Administration (FAA).