The body was spotted by Miami-Dade Police Marine Patrol officers in a Biscayne Bay mangrove swamp accessible only by boat, The Miami Herald reported.
Authorities had been looking for Gerardo Nales since he plummeted from a plane Thursday.
"We're presuming that it's Gerardo Nales, but we're waiting for the medical examiner to positively identify him," police Lt. John Jenkins said.
The newspaper said police, who have homicide detectives assigned to the case, and the Federal Aviation Administration had not identified the pilot or disclosed any information they have about how the two men knew each other or the purpose of the flight. The Herald said other media had identified the pilot as Felipe Fons.
The Piper Malibu took off from Kendall-Tamiami Executive Airport.
"There are still some questions that need to be asked about the circumstances," said Jenkins, who declined comment on a report that Nales is believed to have killed himself.
The pilot issued an emergency call and said his passenger had opened the plane's door and fallen out at an altitude of about 2,000 feet about 8 miles southeast of Tamiami.