Footage shows the culprit placing the flag onto a chair before going to the toilet on it.
He proceeds to wipe his backside with a second Pride flag before leaving the scene.
The incident, which happened at the Buceo 95 bar around 10am on 15 April, is being investigated as a hate crime.
Nathan Nolen Edwards, the venue’s general manager who has worked there for six years, said the establishment has “a very inclusive, largely LGBTQ+-identifying staff” – including drag queens.
“It’s definitely a punch to the gut,” he told the New York Post. “We certainly haven’t experienced anything to this degree. A defecation on a Pride flag is not the norm here.”
READ MORE: Woman arrested on hate crime charges for setting fire to Pride flag in NYC
Bueco 95’s owner, Courtney Barroll, told the aforementioned outlet that the incident “angered” her and she intends to hang even more Pride flags because of it.
“I said, ‘Don’t worry, because for the two flags that he has taken from us, I will put 50 more up, and I’ll wallpaper the whole restaurant with them,’” she explained, referring to what she told her staff. “They all burst out laughing, and said ‘We know you.’”
The New York Police Department (NYPD) shared a video of who they believe to be the culprit on their Instagram tips page with an advertised reward of up to $3,500 (£2,800).
Anyone with information about the crime is asked to call 800-577-TIPS or anonymously post a cop on crimestoppers.nypdonline.org.