The 53-year-old was shot 10 times outside his Staten Island home last week. Cali was allegedly the head of the Gambino family, one of the five Italian-American Mafia families that have historically dominated organised crime in New York and New Jersey.
Anthony Comello, 24, was detained in New Jersey and appeared at the Ocean County Courthouse in Toms River, New Jersey, at 2.30 pm.
Mr Comello wore a green and white jump suit during his appearance, which was a preliminary affair that included a reading of the charges he faces and rights.
Before the hearing, Mr Comello's lawyer indicated that his client would sign extradition papers, putting him on the fast track to be returned to New York for trial.
The case, involving a top mob boss, has captured the imaginations of observers of the mob world.
But, it may turn out that Mr Comello was not allegedly motivated by suspect business, with multiple reports noting that he was romantically interested in the mobster's niece.
Cali, according to those reports, would not allow Mr Comello to date his niece.
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