John Freeman, 16, and 18-year-old Tyler Best were arraigned Tuesday morning in Niagara Falls City Court. A coroner says the little girl died of "asphyxiation due to mechanical obstruction of the airway and compression of the neck."
The arrests came after Best came to police Monday morning and led them to a garbage can containing a trash bag holding Isabella's body. He told them he had helped Freeman dispose of it after Freeman had killed her, police said.
Appearing in a pale blue prison jumpsuit, Freeman and Best entered not guilty pleas. Freeman was charged with murder, as an adult, but both may be eligible for youthful offender status at a later date, court officials said.
Best was charged with a misdemeanor related to helping Freeman dispose of the body.
Isabella's family had called police Monday morning to say she was missing from her great-grandmother's Niagara Falls home, where she'd been staying overnight. Isabella's great-grandmother said she'd last seen her Sunday night with Freeman, a neighbor and family friend.
Authorities said it appeared Isabella had been killed without any weapons being involved.
Police have charged Freeman as an adult, and he faces a murder charge. Best is charged with tampering with evidence.
At a news conference Monday afternoon, Niagara Falls Chief Detective William Thompson said there were signs of injuries but no indication of sexual abuse.
WEB EXTRA: Hear the Police Briefing
"As far as we know, he was a trusted family friend," Thompson said. "It's a terrible crime. It tears at your heart."
Of Best going to police, Thompson said, "I imagine it was his conscience."