The differences are two fold.  First, Pele and Jordan didn't have the second, and arguably third greatest players of all time playing at the same time as Federer has, to reign in your accomplishments.  Secondly, Pele and Jordan don't play one on one against their chief rivals.  I would argue a measure of greatness is playing opponents one on one and consistently beating them, despite different styles, different ages, different court surfaces.  Fed has mastered them all (remember Fed has only one French title, but an additional 5 finals at the French.  Aside from Nadal, and Borg, he is one of the top clay players), and he's now doing with a reborn backhand at 35-36 years of age.  That is phenomenal,