The Illinois Department of Natural Resources said divers recovered the second body from the river near Pulaski Road. The other two boaters are still missing.
Two of the men on that boat have been identified, but officials have not identified the body recovered Friday.
The 26-foot recreational craft that was carrying four people crashed sometime between midnight and 5 a.m. Wednesday, Illinois Conservation Police Sgt. Joshua Mooi said.
Crews recovered the boat but none of the missing boaters were initially located, Mooi said. The vessel was badly damaged when it was located.
The first body was recovered several hours after the crash was reported, about three miles from where the boat was found. The victim was identified as Elmer Jimenez, 32, of East Chicago Indiana, according to Illinois State Police.
"I just saw the boat; whatever they hit, they hit it hard," said Joanna Feliciano, Jimenez's fiance. "I don't know what they hit yet but that boat is... it's in bad shape. Whatever they hit, they hit it hard."
She also said Jimenez was a boat mechanic.
Raul Cazares got the phone call Wednesday that his 40-year-old son, who shares his name, went missing on the Chicago River near Damen Avenue on the city's South Side.
"I was on the highway just freaking out, going crazy," Cazares said. "I asked God, don't let it be true."
"I just miss him right now," he added. "I just want him home and I know if he is not alive I want his body so I can put him to rest."
Crews continue to search for the other boaters.
"Do prayers for me so they can find his body," Cazares said. "We need closure so we can put our kids to rest."
Raul Cazares, Jr., is a married father of six. His family said his youngest child is just two years old.
"He was a fun-loving person," Cazares said. "He loved having friends. He loved being around people. He loved his family. He loved everything about life."
The Sun-Times Media Wire contributed to this report.