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The 43-year-old boxing legend retired from the sport in 2017 after he notched up an undefeated record of 50-0.
Speaking to Fat Joe on Instagram Live, 'Money' said his top three would include himself, Pernell Whitaker would be second and Roberto Duran would rank third.
However, Mayweather then revealed he would pick Larry Holmes ahead of any heavyweight in history.
The future boxing Hall of Famer explained: "We're going to have to go, OK, we'll go 'Money' Mayweather, we got to go Pernell Whitaker, imma go Roberto Duran -- man, you put me in a tight predicament.
"As far as with the heavyweights, if we're going to go heavyweights, I'm going to be honest, I've got to go Larry Holmes."
Fat Joe insisted that he doesn't believe Holmes is better than boxing legends Ali or Mike Tyson.
But Mayweather went on to provide the full "breakdown" behind his decision to pick Holmes for his No 4 spot.
"Larry Holmes beat everybody in his era, when Larry Holmes got beat by Mike Tyson, he got beat by a young hungry champion and he came out of a years retirement and got beat by Tyson," he said.
"I've got to say Larry Holmes, he had the basic fundamentals, he had the jab and even right now he's still living a great life because he made smart investments.
"So he was good from the beginning of his career to the end of his career."
Mayweather's final pick on his top five went to Aaron Pryor, who he claimed only "lost a fight [...] because of drugs."
He told Fat Joe: "Aaron Pryor, the only reason why Aaron Pryor lost a fight was because of drugs, he lost only one fight because of drugs."
Mayweather previously named Ali in his top five boxers of all time during an appearance on ESPN, though he did rank the 'Greatest' at the No 5 spot.
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