2011-Present
Slams: Novak 7, Rafa 5, Andy Murray 2, Stan Wawrinka 1, Marin Cilic 1
Year-end #1: Novak 3, Rafa 1
World Tour Finals: Novak 3, Roger 1
Masters: Novak 15, Rafa 9, Roger 6, Andy 3
Total Titles: Novak 31, Rafa 21, Roger 17, Andy 15
Clearly Novak has the edge over Rafa. But a couple things to consider:
1. An "era" is a subjective time span. If we extend this to 2010 then we're going to see that gap not only narrowed but in some ways Rafa gets the edge (e.g. his Slam count goes up to 8, edging Novak's 7).
2. While I have argued that staying healthy is a skill and that we shouldn't use injury as an excuse, it does bear mentioning that Rafa has struggled over the last few years. When he's been healthy he's at least been Novak's equal, except in the case of 2011.
All that said, I would be surprised if Novak wasn't the top player for the next few years. As I've said before, I see something akin to the status quo--with gradual decline from Roger and Rafa (if in different ways)--for two or three years, and more and more upsets. Then, gradually but perhaps most clearly in 2018, the baton will be passed to the Kyrgios-Coric-Zverev-Kokkinakis generation, when those guys enter their primes.
To put that another way, Nadal, Djokovic and Murray will be entering what is historically the "rapid decline phase" of their early 30s at the same time the younger kids are entering the early prime years of their early 20s. As I wrote elsewhere, here is the age the various players turn in 2018:
Nadal 32, Djokovic 31, Murray 31
Nishikori 29, Raonic 28, Dimitrov 27, Thiem 25, Vesely 25
Kyrgios 23, Coric 22, Kokkinakis 22, Zverev 21
My guess is that those two factors, along with the late peaks of Nishikori-Raonic-Dimitrov, not to mention Vesely-Thiem, should see a tidal shift. Even if Novak and Andy (and perhaps even Rafa) maintain a high level into their 30s, tennis--all professional sports, really--is a game of inches, so just losing a bit and the younger players gaining a bit will see the shift happen.
2018 - mark your calendars! But that's several years away yet. Again, my prediction is that Novak remains the top dog for two or three more years with more upsets from non-Big Four players in the transitional period of 2015 to 2017.
Actually, I wouldn't be surprised if 2015 is something of a "return to full dominance" by the Big Four, with them taking all the Slams and leading people to believe that last year was an aberration. But I think the gap will continue to narrow, and that by 2016 or 2017 we'll see a wider field. But the balance of power won't have fully shifted until 2018.