Maybe YE#1. Djokovic 2015 deserves a good run there, given how he reached nearly every single final of every tournament he entered.
YE#2 best season still goes to Djokovic.
Djokovic 2016 Slams: W W F R3
Federer 2017 Slams: W W QF A
Djokovic clearly ahead in slams.
Djokovic 2016 Masters: W W W W F SF QF R2
Federer 2017 Masters: W W W F A A A A
I think Djokovic comes out ahead here, too. Had Federer played clay, he surely would have lost early, and in any case, winning at least 1 round is better than an absence.
Djokovic 2016 500s: QF
Federer 2016 500s: W W R2
Federer way ahead here.
All in all, Djokovic comes out ahead in this category unless Federer wins the WTF. If he does, then Federer 2017 will be the greatest YE#2 season in history. Until then, no.
As for #3, any really good season by a player who won a slam will suffice. Federer won no slams in 2015, so he can't be the greatest #3. Maybe Murray's 2013 or 2012. That's just off what I can remember. Historically, there's probably been better #3s.