Anthony Comello, who has grown a full beard since his arrest, pleaded not guilty in the shooting death of Francesco "Frankie Boy" Cali.
A bail application will be made later, and attorney Robert Gottlieb asked that Comello remain in protective custody.
"This defendant allegedly wantonly and willfully took another life in cold blood and has now been indicted for murder and weapons charges," District Attorney Michael McMahon said. "This type of senseless violence will not be tolerated in our Staten Island neighborhoods."
Comello made his initial court appearance in New York City last month after being extradited from New Jersey. At that time, Gottlieb claimed his client is a right-wing conspiracy theorist who was influenced by online hate speech.
At his extradition hearing, Comello appeared in court wearing a green and white jumpsuit and had handwritten pro-Trump slogans on his palm, which he held in the air while waiting for the hearing to begin in Toms River.
On it were scrawled pro-Trump slogans including "MAGA Forever," an abbreviation of Trump's campaign slogan "Make America Great Again." It also read "United We Stand MAGA" and "Patriots In Charge." In the center of his palm, he had drawn a large circle. It was not immediately clear why he had done so.
Gottlieb said Comello intentionally showed his hand with scrawlings indicating the far-right conspiracy theory.
"That was real," he said. "That was real. That was what he wanted to express that day. It is not, when I raise the issue of the internet, the hate that is on the internet. It was not just to raise a potential defense."
Sources have previously told Eyewitness News that Comello was dating Cali's niece, a relationship Cali did not support.
Cali was gunned down in front of his Staten Island home after a car accident that investigators believe was staged to lure Cali from the house.
Once Cali came outside the home, sources said, a video showed the two men talking and then shaking hands. Apparently, Cali sensed no danger because he turned his back on his killer to put the license plate inside the rear of the SUV.
That's when the gunman took out a 9-mm handgun, held it with two hands -- as if he was trained, the sources said -- and opened fire.
Cali's wife and child were in the home at the time, which sources say is a highly unusual circumstance in the lore of organized crime -- which, in its heyday, followed certain rules that kept targets from getting whacked in front of their families.
It was the first time a reputed mob boss was killed in New York City in more than 30 years.
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