Fed's was not a comeback. Nevertheless, the way he set about getting to no.1 through planning his schedule (he was not so arrogant as to only enter Slams and MS either; unlike others, I admire that about him, he really enjoys playing), and did it even though Djokovic was at his highest level ever.
While Nadal's run has been scary good, I think most people did not expect him to flop miserably, while hardly anyone expected Fed to return to no. 1 at his age. I will go with Federer here, even though it wasn't technically a comeback.