Francesco "Franky Boy" Cali, 53, was found with multiple gunshot wounds to his body at his home in the borough's Todt Hill section just after 9 p.m.
Cali was taken to a hospital where he was pronounced dead. There have been no arrests.
No other information was provided by police.
Federal prosecutors in Brooklyn had referred to Cali in court filings in recent years as the underboss of the Gambino organization, related through marriage to the Inzerillo clan in the Sicilian Mafia.