Federer's prime was 2003-2009 IMO. His peak years were obviously 04-07. Federer 2 years past his prime still won 2 slams in 09 and was a hair from a 3rd? So yeah, his prime was 03-09, peak 04-07.
Nadal's prime began in 05, I agree there, but to say a guy who's still #1 and still making multiple finals isn't in his 'prime' is ludicrous. Nadal's still in his prime, though it remains to be seen if he still has the peak form he had in 08, beginning of 09, and 2010. Even though Nadal may not still be at his peak (and again, that still remains to be seen, if he wins RG/Wimby double again it would be hard to argue he isn't at his peak), he's still in his prime and should still be able to compete and defeat Djokovic on his favorite surface.
FWIW Djokovic's prime started in mid 07, when he made RG SF, Wimby SF, won Canada beating Nadal, Roddick, Fed, and then made USO final. Your prime doesn't automatically start when you win your first slam, there can be results prior to the first slam that indicate that you are at or near your priime. If Murray wins Wimbledon this year I guess his prime would start then, ignoring the multiple MS titles and slam finals he's made prior to then? :?