Robert Larson, 47, of Westchester found the body among some longs along the west bank Tuesday while searching the river in his kayak, the Chicago Tribune reported.
"I swung around and came back and noticed the body of a baby face-up," said Larson, who spent weeks looking for 1-year-old Bryeon Hunter.
Cook County Sheriff Tom Dart said he anticipated the remains would be confirmed by the medical examiner's office as those of the missing child, the newspaper said.
Lakeshia Baker, 22, and her boyfriend, Michael Scott, 21, who initially reported the child had been kidnapped, are jailed on murder charges.
Scott allegedly beat the boy with a belt and plastic clothes hangers April 15 and left him to die on the bathroom floor of their Maywood apartment, authorities said.
The couple allegedly confessed to disposing of the body but have given conflicting accounts, authorities said.