Officers recovered a weapon from the scene but friends of the 18-year-old say he did not have a gun.
"We was riding our bikes. Out of nowhere the police started coming up and police asked, do we have a gun on us and we said, sir we don't have no gun. My friend, they started chasing one of my friends," said Delano Walker, victim's friend.
Police say the teen did have a gun and threatened officers with it.
The man shot by the officer was taken to Mount Sinai Hospital, and nursing supervisor Toni Hamilton said he was pronounced dead a short time after his arrival.
Area detectives and the Independent Police Review Authority are investigating the incident.
The Associated Press contributed to this report.