William Roberson, 51, was taken into custody Monday and charged with criminal mischief.
Police said Roberson was seen on video smearing white paint across the gallery's front window on May 31.
The gallery was vandalized two more times on June 1 and 2, but he was not charged in those incidents.
The NYPD Hate Crimes Task Force investigated whether the crime was racially motivated, but police now say it stemmed from a previous dispute between Roberson and someone at the gallery.
"I'm neither shocked nor surprised that merely three days after opening on 26 Mercer Street in celebration of our ancestors that we would find a literal white washing of Black Wall Street on our front window," Dr. Ricco Wright, who owns the gallery, said at a rally after the latest incident.
The gallery features work by Black artists commemorating the victims of the 1921 Tulsa Race Massacre.
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