It comes down to another boring "What is talent?" conversation.
McEnroe did things on the court that you would never train someone to do....just look at his forehand and backhand technique, and obviously the serve. The fact that he was able to become one of the all-time greats of the sport with technically awkward shots like that makes him supremely talented in my opinion. If nothing else he definitely was unique and had among the best hands of any player ever.
Federer does a bunch of things that McEnroe never could have done, partially aided by string technology. That forehand is really something special. His ability to take the ball so early so often is also very impressive. In peak form, his footwork was perhaps the best i've ever seen. The rest of his game isn't very unique really, but he still executes at an extremely high level. He's definitely supremely talented, and his results show that.
I would choose McEnroe simply because I like him more. His uniqueness is something that won't be duplicated.
I voted Mac to even things up and it is very close, but in fact Mac's inability to adapt to the power game should decide things in Federer's favour. Roger would have done better with wooden racquets in the 1970s than Mac did with graphite in the late '80s.