According to police and the family, Bruno Valenzuela, 34, was caring for Maverick, 5, in the boy's parents' Port Jefferson Station home on Dec. 20.
Officials said the boy started coughing and crying when Valenzuela aggressively slapped the child on his back and chest, leaving the kid with bruises.
The boy's father, Christopher Brower, said Maverick has cerebral palsy, complex medical needs, is nonverbal and non-ambulatory.
The family took the child to Stony Brook University Hospital two days later to document the injuries, both the family and officials said.
On Dec. 22, the family filed a police report and Special Victims Unit detectives with the Suffolk County Police Department began to investigate.
Surveillance video given by the family to News 12 from cameras that were installed inside Maverick's bedroom showed the nurse allegedly striking, grabbing and roughly handling the child for several minutes while the parents were out of the house.
Last night, just after 9 p.m., Suffolk County police arrested Valenzuela at his home in Brentwood.
Valenzuela was employed at the Christian Nursing Registry in Smithtown, but has since been fired.
Christian Nursing Registry Director Camille Harlow told News 12 in a statement: "We were horrified. In 38 years, we've never had this happen. He was with that family for 3.5 years and had a wonderful rapport with the family and the child. We've cooperated with every entity that has requested information from us. Immediately, the nurse was terminated and reported to the state licensing department. The father continues to use our agency. We're heartbroken. We love this child. We love this family. We are as heartbroken as Mr. Brower."
Harlow said all of Valenzuela's HR documents were up to date, including a background check. She added that he had been with the company for 3.5 years.
Police charged Valenzuela with endangering the welfare of an incompetent or physically disabled person and endangering the welfare of a child.
Valenzuela pleaded not guilty and a judge issued supervised release with GPS conditions. The prosecutor said the charges were not cash bail eligible.
Detectives are asking anyone who believes they could have a family member who is a victim of Valenzuela to contact the Special Victims Section at 631-852-6184.