Pipitone pleaded not guilty to the charges, said his attorney Kevin Kearon.
"He absolutely, positively, 100 percent denies the allegations against him," Kearon said.
"There have been many many proven cases of false allegations of child abuse, this is one such case."
Police arrested the 31-year-old Commack resident earlier this month.
Suffolk County prosecutors say the man abused the boys while working as a home care aide. They say that since 2005 he also has worked as a substitute special education teacher for the Developmental Disabilities Institute and the Deer Park and Smithtown school districts.