Federer dominated the weakest era of men's tennis ever, until Nadal came up and absolutely destroyed him...
Djoko has had it much easier with Nadal falling off a cliff with his body quitting on him the last couple years, and Fed being an old man. Probably the toughest competition period of post 90s was 2007-2012 when Fed and Nadal were both still in their primes, and Djokovic and Murray were entering theirs.
Federer still easily the GOAT, even if Nadal dominated him. Nadal's longevity issues and lack of time as world no 1, keep him just below Fed. Djoko could catch Fed, if he keeps rolling, and that looks likely with the game so weak right now.