When we talk about H2H supremacy between these 3 greats, we have to consider various factors + their ages. Federer is 5 years older than Nadal and 6 years older than Djokovic. That should make him clear underdog against the other 2. However, Federer still makes it close against Djokovic and beats Nadal everywhere outside clay. That should be an indication of the following facts;
1) Peak for peak, Djokovic v Federer with RF97A is even, or Federer has the edge by slightest margin. Being 6 years senior at the age of 38, Federer still pushes Djokovic all the way and sometimes beats him. I have never seen Federer as tired as he was during the 5th set of Wimbledon 2019 final, and that should make it clear he is physically nowhere near his prime. However, Federer is still physically fit, strong and quick enough to beat most of the other players who are just not as good as he is. In Djokovic, however, we have a player who is just good as Federer but 6 years younger, so Djokovic is expected to beat 38 yo Federer quite comfortably, but the fact that it is so close most of the times and, in fact, Federer beats him sometimes suggests that they are almost equal or Federer is better by the slightest margin of the two. These guys are like Mayweather and Pacquiao of boxing, still able to beat the best of the young and prime champions while being in their 40s themselves. Obviously, they are slower and physically not as good as they once were, but modern science has kept them in decent condition still, just enough to make them competitive at their advanced ages. If Hopkins is any indication, Mayweather and Pacquiao can maintain their supremacy well into their mid 40s. I don't know how that can translate into tennis, since tennis is a different sport from boxing, but it may be possible for Federer to stay relevant for another couple of years. We'll find out in due time, but that doesn't mean Federer should be expected to be at the same stage of his career as Djokovic or Nadal. He is 6 and 5 years older than the other 2 and that should be considered as a big factor when thinking of the peak for peak level of these 3 all time greats;
2) Peak for peak, Nadal has perhaps never been better than either Djokovic nor Federer with this bigger racquet and let's talk about Nadal v Djokovic rivalry first. Since Djokovic entered his prime in 2011, he has been dominant against Nadal and it should be clear. They are 1 year separated in age and that makes age a non-factor when talking about their rivalry. We can simply use their H2H as it is between them because they are from the same generation and not much has changed in their playing style or equipment. It is clear Nadal has been more consistent on clay, especially at RG, than Djokovic, but Djokovic has been better on other surfaces, even though Nadal has more USO titles. If they played at their peak level, it seems Djokovic dominates Nadal everywhere other than clay, but even on clay, they are quite even. Djokovic choked at their FO encounters a few times and lost more, but in other events, peak Djokovic has beaten peak Nadal plenty of times to make anyone confidently say at least they are even, but to be honest, I feel peak Djokovic beats peak Nadal anywhere, including clay. It won't be easy, because these two greats are very evenly matched, but Djokovic seems to have that extra bit of ability to just beat Nadal, even on clay. It seems Djokovic is closely but clearly above Nadal in terms of peak level, even on clay;
3) Peak for peak, when given a bigger frame that he is using now, Federer seems to hold advantage over Nadal everywhere except for clay. It has become clear in recent years since Federer switched to 97 sq inch frame, that heavily one sided H2H in favor of Nadal between these two was probably due to 2 factors - their more frequent meetings on clay and Federer's BH being a liability against Nadal's heavy topspin. When these 2 factors were removed by switching to a bigger frame and not playing on clay, Federer has beaten Nadal in every match except, of course, for their FO 2019 SF encounter, despite Federer being 5 years senior. Nadal enjoyed playing Federer on clay with Federer using a 90sq inch racquet as his advantage for a long enough period to build big H2H lead which eventually became big psychological block to Federer. Of course, it's not like Nadal is much inferior compared to Federer in terms of ability, it has always been extremely close between the two, but at this level, tiny little bit of factors change the outcome completely and that's exactly what has happened in the dynamics between their rivalry.
Overall, peak for peak, it seems Federer with the current racquet is quite even or slightly superior against Djokovic, and superior to Nadal, everywhere outside clay. Between Djokovic and Nadal, Djokovic is better than Nadal everywhere, even on clay, but just choked and lost at RG more than he should've. I think this should be quite an objective analysis of any serious tennis fans, peak for peak, H2H among these 3 greats.