A man flying a drone near the half-marathon finish line in lower Manhattan on Sunday set off a terrorism scare that sent cops scrambling by land, sea and air to investigate the mysterious aircraft, sources said.

The unidentified man, who appeared to be in his 20, was dressed in a gray jacket with the word “grenade” written on it.

Around 10 cops from the NYPD’s Counterterrorism Unit rushed to the area around Pier 15 at 11 a.m. after witnesses reported seeing a drone with a camera attached to it hovering downtown.

A police helicopter and a boat from the NYPD’s Harbor Unit also converged on the area as backup but left after the cops on the ground found the pilot operating the device near the corner of South and John streets.

“There was a NYPD helicopter flying overhead,” said one witness. “The guy was about to walk away when about four police cars came and about 20 cops came out. They had counterterrorism jackets on.”

The man was questioned at the scene before police officers patted him down and put him in the back of an unmarked police car and driven away.

The drone was hovering near the finish line of the United Airlines NYC Half-Marathon, which kicked off at 9 a.m. in Central Park.