He was pronounced dead at a hospital soon after.
Gotti, who later died in prison, took over the Gambino family at the time.
"The Gambino crime family during Castellano's reign was the largest criminal organization in the US, with law enforcement estimating it had some 250 "'made" members" and "more than 550 lower-ranking "associate' members".
The last Mafia boss to be shot to death in New York City was Gambino don Paul Castellano, assassinated on Gotti's direction while getting out of a black limousine outside a high-end midtown Manhattan steakhouse in 1985.
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Cali, who was born and raised in NY, was the nephew-in-law of John Gambino and the great-nephew of Bonanno mobsters Vito Bonventre and Giovanni Bonventre.
Cali's wife and children were home at the time of the shooting.
Witnesses reported seeing a blue pickup truck speeding away, police said.
According to the Associated Press, court documents referred to Cali as the underboss of the Gambino crime family.
"It takes a certain type of evil to murder a friend in their own home, and then console the grieving relatives", said Federal Bureau of Investigation assistant director in charge William Sweeney.
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John Vandemoor, a former Stanford University sailing coach, is also scheduled to plead guilty to racketeering conspiracy charges. No students were charged, with authorities saying that in many cases the teenagers were unaware of what was going on.
Authorities believe Cali, who has kept a low profile in comparison to his predecessors, had ties to the Inzerillo mafia family in Sicily.
The day after Castellano's December 1985 murder, The New York Times called the Mob boss' death "highly stylized", but Giuliani dismissed such morbid romanticism.
Following Castellano's murder, Gotti headed the Gambino family until his incarceration for conspiracy and murder in 1992. The 85-year-old was serving a 100-year federal prison sentence after his conviction on racketeering and murder charges in the famous mid-'80s "Commission trial". Sylvester Zottola, 71, reportedly of the Bonanno crime family, was gunned down at a McDonald's drive thru in the Bronx last October, according to WABC.
Otherwise known as "Franky Boy", Cali was considered the de facto godfather of the Gambino crime family, having served on its ruling panel for several years. At a 2008 bail, a prosecutor said Cali was seen "as a man of influence and power by organised crime members in Italy".
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