Surveillance video showed three people smearing blue paint on the Fifth Avenue mural while a woman littered it with flyers around 4 p.m. Friday, police said.
Officers found the trio near the mural a short time later with blue paint on their hands and clothing, police said.
They were arrested, charged with criminal mischief and released with a order to appear in court at a later date.
The woman, 64, was issued a criminal court summons for illegal posting of flyers.
Meanwhile, police are continuing to look for a man in black shorts and a dark blue T-shirt who was seen splashing red paint on the mural around noon on Monday.
The words “Black Lives Matter” have been painted on streets in New York and elsewhere in recent weeks to show support for the movement demanding justice and reforms after the recent police killings of George Floyd and other Black people.
Mayor Bill de Blasio helped paint the mural in front of U.S. President Donald Trump’s namesake tower last week.
Trump complained last month in a tweet that affixing the words to Fifth Avenue in front of his building would denigrate “this luxury Avenue.”