State police dug up the remains of Justin Kowalczik after his mother, Heather Kowalczik, told authorities he had died in the summer of 2010 and was buried on the property, WNYW-TV, New York, reported.
The family never reported the child's death, which police said occurred about the time they moved into the Farmingdale neighborhood from Orange County. How he died had not been determined, the TV station said.
The family has two other children.
The revelation of the boy's grave came as Child Protective Services began to investigate the mother and her boyfriend, Robert Rodriguez, following an injury suffered by her 6-year-old child.
No charges had been filed in the case, but WNYW-TV said that could happen soon.
Kowalczik was questioned and released, while Rodriguez, who is not Justin's biological father, was considered a person of interest, the TV station said. He has refused to cooperate with police, the station said.
Rosie O'Donnell unveils nearly 50-pound weight loss
Putin thinks Obama would save him if he were drowning