Video footage purportedly showed the officer using the banned technique as the man was restrained on a boardwalk at Rockaway Beach in Queens on Sunday, SkyNews reported.
The NYPD released its own body-camera footage of the incident and said an “active use of force investigation” was under way.
The incident follows widespread protests in the US and around the world in recent weeks sparked by the killing of George Floyd in Minneapolis while in police custody.
The New York officer was one of four involved in detaining the man, who can be seen lying face down on the ground during the incident.
A video shot by someone at the scene showed the officer putting his arm around the man’s neck as a person yells: “Stop choking him, bro… let him go.”
As the man lies still on the ground, another person can be heard saying: “He’s out… look, look.”
The officer relaxes his grip after a fellow officer taps him and pulls on his shirt.
The incident happened at around 8.45am local time on Sunday after officers responded to reports that three men were harassing people and throwing objects at them, sources told NBC News.
Officers attempted to make an arrest after one of the men approached the officers with “a small bag” which they thought he would throw, the sources said.
The NYPD said the arrested man suffered minor injuries, NBC News reported.
The NYPD banned chokeholds in 1993 and their use has been especially fraught since the 2014 death of Eric Garner after an officer put him in a chokehold while trying to arrest him.
New York Governor Andrew Cuomo recently signed into law a package of police accountability measures including a ban on chokeholds following protests over Mr Floyd’s killing.
US President Donald Trump signed an executive order last week restricting the use of police chokeholds, saying they will be banned “except if an officer’s life is at risk”.