Federal prosecutor Robert O'Neill announced the indictment of the 44-year-old Gotti and five other men at a news conference this morning.
Gotti - the son of the late Gambino family crime boss John Gotti - is expected to appear later today in Manhattan federal court.
O'Neill said the slayings occurred in 1988, 1990 and 1991.
If convicted, Gotti faces life in prison.
Gotti was nabbed Tuesday morning in New York at his Oyster Bay, Long Island home, CBS Station WCBS-TV reported.
He will be arraigned later Tuesday from Lower Manhattan, law enforcements said.
Gotti was tried three times in Manhattan on racketeering charges for an alleged plot to kidnap Guardian Angels founder Curtis Sliwa.
The trials in 2005 and 2006 ended in hung juries and mistrials, and federal prosecutors announced a year ago that they were giving up.
A call to Gotti's attorney was not immediately returned.