Very difficult as so many variables, not all objective and clear. Tried to focus mainly on achievements rather than on overall level of play, otherwise I would have ranked it differently. I also only ranked YE #1 so no Djokovic 2016 or Fed 2017 for example. Many of the below are interchangeable and might have been different had I ranked it tomorrow:
D 2015 - 3 slams with a final. YEC. 6 masters with 2 finals. Decent win loss ratio at 82-6. Other impressive qualities include 31 top 10 wins and big titles on all surfaces.
F 2006 - 3 slams and a final. YEC. 4 masters and 2 finals. Very impressive 92-5 win loss ratio. No big titles on clay, but faced prime Nadal there
D 2011 - 3 slams, 5 masters. No YEC but dominated Fedal. Decent win loss at 70-6. Fell off a cliff towards the end but only 2 losses from AO to USO winning first 41 matches.
F 2004 - 3 slams, YEC and 3 masters. Good win loss at 74-6. Undefeated against top 10 and in finals. 11 titles
F 2007 - 3 slams and a final. YEC. 2 masters and 5 finals. 8 titles and 68-9 win loss. A stepdown from the above outside slams but at slams, can't get much better
N 2010 - 3 slams. 3 masters. YEC final. Really difficult to rank. Definitely below the above, but you could make good arguments for 2 slam seasons above it. Ultimately, 3 slams on 3 surfaces does enough for me. The clay slam was very impressive also
F 2005 - 2 slams and 4 masters. YEC final. Insane 81-4 win loss with 10 titles puts this at the top of the 2 slam years for me.
N 2013 - 2 slams, 5 masters. YEC final. Difficult to pit against Nadal 08. Arguably higher level there, but 2013's win loss of 75-7 and 10 titles edge it
N 2008 - 2 slams, 3 masters. OG. Channel slam against Federer very impressive. His whole summer was peak Nadal
F 2009 - 2 slams with 2 finals, 2 masters. Definitely good arguments for 1 slam seasons above this but 2 sets away from CYGS is very impressive. Channel slam as well.
N 2017 - 2 slams with a final. 2 masters. In terms of level of play, this would rank below other 1 slam seasons. In terms of overall achievement, this one gets the edge over them
M 2016 - 1 slam with 2 finals. YEC. 3 masters. OG. 78-9 win loss ratio. 9 titles. Clearly the strongest of the 1 slam YE#1s. Just a little too strong to be below Djokovic 2018
D - 2018 - 2 slams, 2 masters. YEC final. Really tough to rank. Part of me feels it should be bottom. But 2 slams is very impressive. And he still managed to win 2 masters and reach YEC final so it's not as though he did nothing outside of slams
D 2014 - 1 slam with a final. YEC. 4 masters.
D 2012 - 1 slam with 2 finals. YEC. 3 masters with 3 finals. In terms over overall level for Novak, probably 4th after 2015,11 and 16. In terms of achievements, probably his weakest YE #1
The weaker 2 slam years vs the 1 slam years is really murky territory. As I said before, this is not my opinion on level of play. It was considered, but given very low weighting
Sorry for v. long post!