Businessman and philanthropist Alphonse Fletcher, Jr. - a former president of the Dakota's co-op board - claims his request to expand his apartment in the building was refused because he is black.
He is suing the officials over what he calls "an extensive pattern of hostility toward non-white residents of the building".
Fletcher names Banderas in his suit, claiming he overheard a conversation between two board members discussing the Spaniard's efforts to buy an apartment at the Dakota.
He suggests the unnamed neighbours refused to even give the actor and his wife Melanie Griffith an interview, joking they wanted a first-floor pad so Banderas could "purchase drugs from the people on the street".
Fletcher also names singer and neighbour Roberta Flack in his suit, claiming she was refused permission to install a new bathtub because she's black.
The plaintiff is demanding damages of $15 million (£10 million).
The Dakota Building's most famous resident was John Lennon, who was shot dead on the pavement outside in 1980.