There were no arrests and the investigation is ongoing, the NYPD said.
The 53-year-old, thought to have been de facto godfather of the Italian crime family since 2015, suffered "multiple gunshot wounds to the torso" in the attack on Wednesday evening, police said.
Police confirmed the identity of Cali, who was pronounced dead at Staten Island University Hospital.
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. But he apparently ascended to the top spot in 2015, although he never faced any criminal charges that said so.
This is a breaking story. He died in prison in 2002.
DeCicco was the No. 2 figure in the Gambino family in 1986 when he died in a vehicle bombing in Brooklyn.
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A law enforcement official confirmed to CNN that the victim was a high-ranking member of the Gambino organized crime family and is believed to be the acting boss.
In 1992, Gotti was convicted in Castellano's murder and a multitude of other crimes.
Aggressive federal prosecutions in the past 25 years decimated the ranks of New York's five Mafia families.
Cali kept a much lower profile than Gotti and was killed in far less spectacular fashion than Castellano.
Pandrella, 59, is accusing of shooting Zito in his own home and stealing money from him - before returning to the scene of the crime hours later to grieve with the older man's family.
Last October, 71-year-old Sylvester Zottola of the Bonanno family was shot dead while waiting in his vehicle for an order from a Bronx McDonald's. On April 6, 2009 he was released from prison.
Last week, Carmine Persico, the 85-year-old former boss of the Colombo organisation, died after serving 33 years of a 139-year prison sentence.
Four days before the meeting, "On The Inside" reported that Cali was the choice among his comrades, who respected Cali's strong low-key, old-world approach to doing business successfully without attracting fanfare or agita.