McEnroe, a seven-time Grand Slam singles winner, called Williams "best female player ever -- no question," in comments to National Public Radio aired Sunday.
But asked why she should not be considered the best of all time, McEnroe added: "If she had to just play the circuit -- the men's circuit -- that would be an entirely different story."
McEnroe, speaking on a tour to promote his new book "But Seriously," said he would place Williams "like 700 in the world" on the ATP Tour.
"Dear John, I adore and respect you but please please keep me out of your statements that are not factually based," she wrote.
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"I've never played anyone ranked 'there' nor do I have time. Respect me and my privacy as I'm trying to have a baby. Good day sir."
Williams, 35, won this year's Australian Open for her seventh Melbourne crown and her 23rd Slam singles title, setting an Open Era record and moving one shy of Margaret Court's all-time Slam singles title record.
In April, Williams announced that she was pregnant and would not compete for the remainder of the season.
McEnroe, 58, is a former world number one like Williams. He won four US Open and three Wimbledon singles titles.