At a press conference Saturday afternoon, Chief of Detectives Dermot Shea announced Comello's arrest, but said such issues as motive and possible accomplices were still under investigation.
The 53-year-old Cali, who was shot to death on Wednesday outside his Staten Island home, was allegedly the head of the Gambino family, one of the five Italian-American Mafia families that have historically dominated organized crime in NY and New Jersey.
Police were searching for the pickup truck that raced from the grisly scene, sources said. Shea said Cali was shot 10 times.
Shea said there was "extensive video footage" recovered from the house where the shooting occurred.
"We thought those days were over", the city's Mayor Bill de Blasio told journalists after the shooting.
"We do not believe this was a random act".
Shea didn't give details about how Comello became a suspect.
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A white male, 24, who is a Staten Island resident and was apprehended in New Jersey on Saturday morning, is being questioned in the Garden State about the murder, law enforcement sources told the Advance. "I only spoke with him in passing when we stopped to say hello", Victor Ujeck, a neighbor of Comello, told Staten Island Advance.
Shea declined to say if Comello had a criminal record, but said he had "crossed paths" with the NYPD.
While Shea said investigators have not ruled anything out, even probing whether Comello was hired to kill Cali, several sources said this didn't seem to be a traditional organized crime hit, believing it was something more personal.
Cali was an associate in the Gambino family, according to court documents, when he was indicted in 2008 with more than two dozen other Gambino members for a range of alleged crimes.
Cali was released after 16 months in federal prison in April 2009 for an extortion scheme.
Cali, a native of the Italian island Sicily, served in the organization's ruling panel for years before replacing Domenico Cefalu in 2015.
The last crime family boss to be shot in New York City was Paul Castellano.