If we just put an extra RG on Novak's CV and nothing else then I think I would. He would still be behind Fed by a couple RG final appearances, but then again, those are kind of offset by Djokovic playing Nadal in 3 RG semis, where Federer only played him once in a RG SF. That's just seeding. The only thing that could be said against this is that I'm kind of assuming that Djokovic could beat Davydenko in 07 or Monfils in 08 if you switched Djokovic and Federer in those draws, and then not really crediting Federer for winning an extra match even if it wasn't against Nadal.
But then Nole's exploits in masters are a little better. They are 5 masters all on red clay, but Federer showed some versatility by winning the one and only on blue clay.
However, Djokovic has won them all and he's also beaten Nadal at Rome, MC, and Madrid, while Federer has only done it at Madrid and Hamburg. And we all know that beating Nadal at MC and Rome is no small feat. Fair edge to Nole here.
And of course, if he managed to beat Nadal at RG, then that goes without saying. So all in all, I'd give it to Novak, yes. I guess it comes down to how much you value a couple extra RG finals for Federer, vs Djokovic beating Nadal to win all the masters. As I said, I would give it to Novak, but I can still see arguments for Federer even if Djokovic were to win RG without beating Nadal.
Honestly, I thought long and hard about this. It's very close.