NY media reported that 53-year-old Cali was shot multiple times outside his vehicle on Staten Island on Wednesday evening, local time, by an unidentified man who then fled the scene in a blue auto.
Cali is the first mob boss to be murdered in NY since Gotti ordered the infamous hit on Gambino boss Paul Castellano, having him gunned down in front of Sparks Steak House in Manhattan in December 1985.
Francesco "Franky Boy" Cali, 53, was found with multiple gunshot wounds to the torso outside his home on Hilltop Terrace in Todt Hill.
Police added he was taken to Staten Island University North hospital, where he was pronounced dead. Investigators haven't made any arrests in the hours that have passed but insists the case remains an open book until they publicly state otherwise.
Cali was sentenced to 16 months in prison and was released in 2009.
Following Castellano's murder, which saw the boss dramatically gunned down outside a Manhattan steakhouse after stepping out of a black limo, Gotti took over as the Gambino family don.
He died in prison in 2002, leaving a notorious legacy that cemented New York's place in mob lore.
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Gambino family mobster Francesco "Frank" Cali has been murdered in what local media say is the first major NY gang killing in more than 30 years. The New York Daily News stated that a family member called 911 and said Cali was run over before he was shot; one witness told the Daily News, "There were like six shots, and then there were three more".
Cali was the first NY crime family boss shot in 34 years, according to WPIX.
NY media say it is the first targeted killing of a mob boss in the city since 1985.
Cali reportedly became the Gambino godfather in 2015 and is said to have brought a new crop of Italians to NY straight from Sicily.
"We thought those days were over", Mayor Bill de Blasio said of Cali's slaying.
Last October, 71-year-old Sylvester Zottola, a reputed associate of the Bonanno organisation, was shot dead at a takeaway restaurant in the Bronx, New York.