Both are now under arrest, charged with failing to report a case of suspected child abuse.
The alleged incident happened at the Children's Village, a 180-acre residential and educational facility for troubled children.
In September a socio-therapist named Clevon Claire was arrested and charged with grabbing a 16-year-old student by the neck and throwing him to the ground.
Edward Rice, a teachers' assistant, was charged with restraining that student's legs during the incident, but his lawyer claims Rice is a decorated employee with 13 years experience.
The incident was captured on surveillance video at the facility which has been operating in Dobbs Ferry since the late 19th century.
Prosecutors say Janet Hotchkiss is seen observing the event, but never filed a report with state officials as required.
Her lawyer insists Hotchkiss did follow protocol by informing a supervisor.
The lawyer for the third suspect, Matthew Magee, claims the Phys Ed instructor witnessed only the end of the incident and thought an unruly child was being restrained, which is not an uncommon occurrence at the facility.