Probably Novak overall, particularly because most of the tour plays a style that plays right into his hands when zoning. He'll just stand on the baseline, run everything down octopus-style, and redirect pace mockingly all day long, and at his peak it's an awe-inspiring display.
On the other hand, Nadal's kill shot FH and accompanying greater capacity to manufacture pace, as well as the margin for error his ground game has, works a little better than Novak against players who like to change the tempo on him (i.e., Fed, Murray, Haas (who's never even won a set against Nadal)), but those are fewer and farther between these days, and it's not like Novak's some slouch against those guys either.
Very close overall, but if given a blind choice, I'd probably take peak Novak's ground game. I go back and forth though.