Nadal's #1 in my book. If we have ATP points or overall titles as the main criterion, 2015 can be considered the best year. But I consider the following criterion as the most pertinent: domination of all surfaces at the Slam level.
Following the aforementioned criterion, this is my list:
1. 2010
2. 2011
3. 2006/2015
5. 2007
6. 2004
Nadal in 2010 became the first and ONLY player to win 3 Slams on 3 different surfaces the same calendar year. Which is the reason why 2010 is for me the best season of a member of the Big 3, it is the only season where a player dominated the 3 surfaces at the Slam level. Only 2011 from Djokovic comes close in terms of domination of the 3 surfaces at the Slam level. In 2015 Novak lost the RG final to Wawrinka, which is unforgivable as it means 2015 was not an all-around dominant year on all surfaces. In 2004 Federer lost in the 4R of RG, so even though his level was very good on hard and grass, I had to donwngrade it because of his lack of succes on clay at Slam level. 2006/2015 are very close with regard to my criterion, so I let them be tied.
Of course, this is my personal criterion. Feel free to elaborate another list following a different methodological criterion.
All this time and you are still hanging on this really thin straw - that is laughable. Domination on all surfaces and Nadal is an oxymoron. He never even made all 4 finals, he had a pretty easy run at RG and Wimbledon, also US Open, out of his measly 7 titles 4 came on clay, and the last one was Tokyo beating a bunch of nobodies. He of course couldn't win the WTF. Didn't reach a Masters final outside of clay losing to the likes of Ljubicic, Roddick, Baghdatis, and Melzer, while his overall record was 71-10.
It was a good season, no doubt, but it's nowhere near top 5 by the Big3, let alone the best ever.