The answer is no, Federer is better than them. His 2004-2007 level will probably never be matched in terms of how consistently great he was, it always took something monumental to take him out or even push him at Slams. He most definitely raised the bar in ways never seen before.
Both Nadal and Djokovic in their peak years would likely dominate Federer's era too (although it's impossible to say for sure), but never to the extent Federer did, which is quite unique in history.
Both Nadal and Djokovic at their best would appear to be better than almost all players active in 2004-6. However, neither of them at their peak has managed to play so well so consistently over such a long period. Nadal has been hampered by physical issues, otherwise, who knows? Djokovic, well, he's still got time to prove us wrong, but it looks unlikely he'll repeat the first half of 2011 again.