The FAA says it was an Augusta A109E helicopter which crashed into the roof of 787 Seventh Avenue.
The FBI is involved in investigations.
The mayor told CNN that the victim was a commercial pilot who was involved in ferrying executives around. He said that it is "very unusual" but "we see nothing criminal" and "no act of terror".
Authorities are checking whether the pilot had authority to fly in the restricted area.
Officials told a press conference that the helicopter was privately owned, that the pilot has been identified and a potential path of the helicopter travel has been identified.
The helicopter was flying in heavy rain in airspace that is supposed to be off-limits.
A flight restriction in effect since US President Donald Trump took office bans aircraft from flying below 914m within a 1.5km radius of Trump Tower, which is just a few blocks from the crash site.
It wasn't clear why the pilot flew into that part of Manhattan, but authorities called it an emergency landing.
Bob Murphy was working on the 47th floor of the 51-storey building when the helicopter crashed into it.
He told Newstalk ZB he initially feared he was hearing a small plane heading for the building.
"It occurs to me that I'm being silly standing by a window, if it's a low-flying struggling prop plane, and maybe it's best I stand back.
"The next thing I know, I hear this huge bang, and it literally shakes the whole building."
Murphy said by the time everyone reached the ground floor, pandemonium had set in with emergency services on the scene.
— Spectrum News 1 Kentucky (@SpectrumNews1KY) June 10, 2019
The pilot was killed in the crash after the helicopter burst into flames.
The pilot was the only person aboard the Agusta A109E helicopter when it crashed about 1.45pm local time.
#FDNY confirms a helicopter has crash-landed onto the roof of 787 7th Ave in Manhattan. The fire has been extinguished, and members continue to operate in response to fuel leaking from the helicopter. There is currently one fatality reported.
The weather in the area is poor, with heavy rain and strong winds.
The damage is believed to have been restricted to the top of the building, identified as the Axa Equitable Centre on Seventh Avenue.
People inside the building had felt a large shake and a fire broke out.
PRELIMINARY UPDATE: There was a helicopter hard landing on the roof of 787 7th Avenue in Midtown Manhattan. Fire has been extinguished. Please continue to avoid the area. https://t.co/pBvrbD1MGh
"If you're a New Yorker, you have a level of PTSD, right, from 9/11,'' Cuomo said.
"I remember that morning all too well."
The Federal Aviation Administration said there was no indication the crash was terrorism-related.
I have been briefed on the helicopter crash in New York City. Phenomenal job by our GREAT First Responders who are currently on the scene. THANK YOU for all you do 24/7/365! The Trump Administration stands ready should you need anything at all.
787 7th ave, #midtown NYC. We’re 1 block south. 20 mins ago there was a loud sound like a too-low #helicopter & I looked up and saw sheet of flame on roof and then smoke. News reports saying helicopter/small plane crash onto roof which would be consistent with what I heard/saw. pic.twitter.com/swY3ksLskH
Videos posted by onlookers showed emergency vehicles in the street, but no obvious damage to the skyscraper, which is about 229 metres tall.
Pedro Rodriguez, a pastry line cook at Le Bernardin, a well-known restaurant in the building, said workers got an announcement telling everyone to exit, and he later heard from people around him that there was a fire on the roof.
The evacuation wasn't chaotic, Rodriguez said, but he was rattled because he immediately thought of the September 11 attacks.
Alex Jacobs was working on the seventh floor when he heard bells and an announcement to evacuate. He and his colleagues - who hadn't heard or felt an impact - used stairs to a fire exit.
"It's really unfortunate. I Just hope everyone's OK," he said.