The small plane was 43 years old, the state-run Notimex news agency reported, citing the Mexican director of civil aviation.
The Drug Enforcement Administration is investigating the company that owned the plane.
Court records showed that the aviation company, Starwood Management, had two planes seized this year. The DEA declined to give further details, citing an ongoing investigation.
But it confirmed that the company was in a dispute with insurance firms over accusations of of falsehoods. Starwood and its representatives have not responded to repeated CNN requests for comments.
The U.S. National Transportation Safety Board said it is helping with the investigation.
U.S. records show the airplane was substantially damaged in 2005 when it struck a runway marker near Amarillo, Texas. At the time, the plane's pilot reported losing the ability to steer while landing the plane.
As the investigation into what caused the crash continues, family members said Wednesday that they were grateful to fans for their support and were committed to honoring Rivera's legacy.
"The best thing you ever taught me is when you fall, you get back up," daughter Jacqie Melina Campos said. "So that's what I'm going to do."
As the ceremony drew to a close, confetti fell onto the stage, and family members and fans covered Rivera's casket with white roses.
A band played the last few bars of "I Will Survive" before a recording of Rivera's voice boomed through the speakers.