The six-year-old, identified as Fajr Williams, was in her wheelchair when she boarded the bus.
Amanda Davila, 27, was assisting children on the bus and secured Fajr's wheelchair inside the vehicle.
Investigators said while the bus was in motion, a series of bumps caused the child to slump in her wheelchair seat. As a result, the four-point harness she was secured with became tight around her neck, preventing her from breathing.
Though Fajr's condition, Emanuel syndrome, a rare chromosomal disorder, left her unable to speak or walk, she was able to make sounds.
Police said Ms Davila was allegedly seated near the front of the bus and was using her cell phone with her earbuds in both ears during the drive.
Wali Williams, the girl's father, said he could imagine his daughter struggling fruitlessly to get help.
“I am picturing her fighting. She can’t speak, she can’t defend herself. She cannot take the things off her neck,” he told WNYTV 7. “I pray that these people weren’t up there lollygagging, playing and joking on their phones while my daughter is back there fighting for her life.”
He said the girl "didn't have oxygen in her brain for almost 40 minutes," in an interview with NBC-4.
"She was the sweetest kid you'll ever meet," Fajr's mother, Nash Williams, told the broadcaster. "She had the sweetest little laugh, little dimples and she just endured so much in her six years. To be taken away from us in such a way, that had nothing to do with her condition."
The investigation noted that cellphone and headphone use was a violation of the policies and procedures of the company contracting Ms Davila.
Mr Williams said that the companies contracted to work with children with disabilities "need to know that when they take that job, they have lives in their hands."
“The most important thing is that we want justice for Fajr,” he added.
Ms Davila was arrested and charged with second-degree manslaughter as well as endangering the welfare of a child.
She has been booked into the Somerset County Jail until her detention hearing.