Witnesses told local media of hearing at least six shots coming from outside, and seeing Cali's family members rushing outside and crying next to his body.
NY media say it is the first targeted killing of a mob boss in the city since 1985. News accounts since 2015 said he had ascended to the top spot. The cases resulted in long prison terms for their bosses - Cali's swaggering 1980s-era predecessor John Gotti included - and encouraged their successors to keep a lower profile.
Chief of Detectives Dermot Shea said there has been a slight urise in alleged mob-related violence in NY within the previous year.
One of the most notorious gangs of NY is at the center of a new mob murder mystery.
USA media reported that Cali's death marked the first murder of a NY mob boss in 34 years, since the death of Paul Castellano - another Gambino family boss - by order of the infamous John Gotti, also known as Teflon Don.
"The Gambino crime family during Castellano's reign was the largest criminal organization in the USA, with law enforcement estimating it had some 250 "'made" members" and "more than 550 lower-ranking "associate' members". Gotti then took control of the family. "The word that I'm hearing is this: That there's old school tension and friction".
Cops retrieve evidence from the scene where Mob boss Francesco Cali was clipped late Wednesday. THE ASSOCIATED PRESS
He was pronounced dead at a hospital.
After prosecutors called him "a danger to the community" Pandrella, 59, pleaded not guilty in Brooklyn federal court to accusations of shooting Zito in his own home and stealing money from him.
Castellano, the Gambino family head at that time, was shot in the street on Manhattan's East Side while on trial for conspiracy to commit murder, among other charges.
Last October, Bonanno crime family associate Sylvester Zottola, 71, was gunned down at a Bronx McDonald's drive-thru as he waited for a coffee. Persico was convicted in a 1986 case overseen by then-US Attorney Rudy Giuliani. Cali served a 16-month prison sentence for the crime.
He says with Cali's killing, he does expect to see more violence in the future, but he doesn't believe there's a target on Gene's back.