At one point officers had to clear the courtroom when the family of the victim, Bella Edwards, started screaming at the defendent, Marc Jenkins, 32, of Seaside.
It happened after Jenkins' attorney asked the judge to place her client in protective custody in jail.
One of Bella's relatives yelled "feed him to the wolves" as they pointed at Jenkins' stepmom and two of his aunts who were also in the courtroom.
During the arraignment, Jenkins looked down and shook his head from left to right.
Jenkins faces up to 25 years in prison if convicted.
Bella was found unconscious and unresponsive in an apartment building on Beach 105th Street around 6 p.m. Monday.
District Attorney Richard Brown said that, according to the charges, Jenkins was the sole adult in the apartment with Bella and her 3-month-old sibling for about eight hours prior to the 911 call.
Emergency responders rushed the girl to a nearby hospital, where she was pronounced dead.
The medical examiner determined that Bella died as a result of blunt force trauma to her abdomen. Investigators are trying to determine whether she was also a victim of sexual abuse.
Investigators believe Bella's mother, Shamikaa Gonzalez, was out all day on Monday. When she returned, her little girl was unresponsive.
Authorities say surveillance video shows Jenkins left the home around 2:30 p.m. with Bella and her 3-month-old sister. But when they returned about two hours later, there was clearly something wrong with Bella.
"We saw the child coming into the building at 4:30," said NYPD Chief of Detectives Robert Boyce. "She appeared to be in some kind of distress, it's hard to articulate. We feel it happened sometime in that car, the assault on this little girl, this little girl was hit about the abdomen. We're looking back, we'll do cell sites, we'll do other things to see where they traveled to, where they stopped at and see if we can get video of any kind of incident somewhere else."
Authorities say the blow to her abdomen was so severe that the girl bled to death.
"Bella, I'm so sorry I wasn't there to protect you," Gonzalez wrote on Facebook. "This feels like a bad dream I can't wake up from. You was loved by everyone and shared so many funny memories. I'm going to miss all the times you kissed and hugged me every day."
A vigil was held Wednesday night at the mother's apartment building in Seaside.
Neighbors were stunned.
"I cant believe it," neighbor Michelle Mevorach said. "I cant believe that because she, you wouldn't be able to see that because she was so sweet. They took very good care of her. She was never in a bad mood, Bella. Always sweet, always happy."
Investigators say Bella's injuries were consistent with that of physical abuse. One neighbor who works as a teacher and is trained to spot child abuse said she never saw anything amiss.
"I'm a mandated reporter, so I would be able to, I would think I would be able to notice these things," Laura Cabrera said. "But very well groomed, very beautiful family."
The 3-month-old sibling was taken to the hospital for evaluation.
ACS Deputy Commissioner for External Affairs Eric Ferrero released a statement:
"Our top priority is protecting the safety and well-being of all children in New York City. As soon as this family came to our attention last night, we immediately launched an investigation with the NYPD, and we secured the safety of the other child in this home."
Authorities say Jenkins served eight years in prison for attempted murder and was released in 2011.
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