Nadal won the Rogers Cup earlier this month and then opted to take a two-week break before the US Open gets underway on Monday.
In that time, Djokovic was put through a gruelling seven days which ended in success as he beat Roger Federer in the Cincinnati Masters final.
The win followed up a brilliant campaign at Wimbledon to install himself as the favourite to win the final Grand Slam of the year.
But McEnroe believes Nadal’s freshness will hand himself the slight advantage in trying to defend his crown in New York.
“A lot of people are saying Djokovic is the favourite,” McEnroe said.
“I actually still think Nadal is the favourite, and he’s my pick to win it.
“I think he played well in Canada. He’s fresh coming in. I think he was smart to miss Cincinnati.
“Certainly one of the matches of the year was the semi-final loss in Wimbledon to Novak.
“But I think a hard court is a better surface for Rafa. Obviously Djokovic is awesome on hard court, too.
“The fact that they played so close at Wimbledon where I think Djokovic is definitely a better grass court player than Rafa, and I think Rafa is going to be incredibly motivated to win it because he sees that he can run down Roger in overall majors.
“Not to mention the fact he wants to keep Djokovic at bay. Those three guys are the clear favourites.”
Meanwhile, McEnroe thinks Federer will need to up his recent performances if he is to put up a serious challenge for Grand Slam No 21.
“I think Roger has looked a little bit shaky in Cincinnati, although a shaky Roger still made to it final,” he added.
“He’s got to try to catch fire. If he can catch fire in week number two, that’s when he becomes super dangerous.”