I would like to see Rafa's h2h vs the top ten during that period vs Novak's and Roger's.
If we take Rafa's peak range as 2008-13, we get:
Rafa: 93-40 vs top 10 (69.9%); 47-26 vs top 5 (64.4%); 115-11 at Slams (91.3%); 406-62 overall (86.8%)
Novak: 99-51 vs top 10 (66%); 48-36 vs top 5 (57.1%); 125-18 at Slams (87.4%); 422-81 overall (83.9%)
Roger: 68-54 vs top 10 (55.7%); 33-39 vs. top 5 (45.8%); 122-19 at Slams (86.5%); 375-82 overall (82.1%)
So from 2008-13, Rafa clearly has the edge - especially over Roger. I mean, those are Rafa's best years and Roger had fallen from his absolute peak, and plus had that one horrible 2013 season in the mix. But Rafa was clearly the best player overall during that period, the "Golden Age" of the King of Clay.
Here's the best six-year spans of the other two, with Rafa's best repeated for comparison:
Rafa (2008-13): 93-40 vs top 10 (69.9%); 47-26 vs top 5 (64.4%); 115-11 at Slams (91.3%); 406-62 overall (86.8%)
Novak (2011-16): 140-34 vs top 10 (80.5%); 66-25 vs top 5 (72.5%); 143-13 at Slams (91.7%); 427-50 overall (89.5%)
Roger (2004-09): 91-30 vs top 10 (75.2%); 44-23 vs top 5 (65.7%); 149-10 at Slams (93.7%); 442-51 overall (89.7%)
So as you can see, Rafa's best six-year span is lower in all categories than the respective spans of both Novak and Roger, but...with a caveat. There's no denying that Roger had more easy wins - his gaudy record at Slams in 2004-09 is certainly padded by more easier opponents (Marcos Baghdatis?). So overall, I think Rafa in 2008-13 and Roger in 2004-09 are closer than the numbers above imply. Roger's span is still more dominant, but it was a dominance held in an overall easier context - especially the first few years before Novak and Andy got going in 2008. Furthermore, note that Roger's and Novak's best six-year spans don't overlap, but Rafa's overlaps with both...so he had to deal with a bit of both during their peaks, with only 2010--the year he won 3 Slams--without a peak-era Roger or Novak. 2008-09 was not
absolute peak Roger, but Novak had a great year in 2008 and Andy was in play, and Rafa had one of his best years in '08 and would have in '09 if not for injury. Roger had one year without a very high level Rafa, and his four best years without a truly peak Rafa; Novak also had a few years without peak Rafa or Roger.
Again, different players of greatness that all point to three truly amazing players, who were all utterly dominant in slightly different ways.
That said, Novak's six year run has some really highlights. What stands out for me is that he played 174 matches vs top 10 opponents - vs. 121 for Roger and 133 for Rafa. And he still had a better win% vs. top 10 players (and top 5 players, with significantly more played than the other two). During their six year spans, Roger won 14 Slams to Rafa's 10 and Novak's 11. But the difference in those numbers is probably mostly--if not entirely--due to easier competition. In other words, if the 2004-09 version of Roger had played in a context similar to 2008-13 or 2011-16, he probably would have won 10-11 Slams too; similarly, the 2008-13 Rafa or 2011-16 Novak would probably have won 14ish Slams in a context like 2004-09.
But what we'll never know is how they would have matched up at their very best. Instead we get (somewhat) overlapping waves, with Rafa and Novak from 2011-13 being perhaps the best example of two of them playing alongside each other in peak form.
If you dice up their careers in different ways, you get different results. Roger has the best 2-4 year spans (any 2-4 year span from 2004-07 is best in class), but starts losing ground after that. If you focus on clay or any single surface, Rafa is clearly the top guy. And he also stands out as being the first to reach close to peak form, at the tender age of 19 (Rafa in 2005 wasn't far from where he got to in 2008-13). Novak has the best single season, and gets the overall title with more truly great seasons than the other two.