The so-called 'Big Three' of tennis have long dominated the ATP Tour, with all three sitting on 20 major titles after Djokovic collected three from a possible four in 2021.
Djokovic, who secured a year-end number one ranking for a record seventh time, would have completed a clean sweep if it were not for Daniil Medvedev in the US Open final.
Nadal, by contrast, missed large parts of the season with a foot injury, while Federer was similarly ruled out for a substantial period after requiring a third knee operation in the space of 18 months.
Nadal could make a return for the Australian Open in January, an event that the world number one may miss due to a vaccine mandate, but he still expects Djokovic to hold the record for major titles when the trio has retired.
"Djokovic is best positioned to be the [men's] player with the most grand slams," Nadal said to Movistar.
"You don't have to fool yourself – Federer is where he is and I am where I am. However, Djokovic is playing well and in a good moment.
"That is the reality, and you can't ignore it. We don't know what is going to happen in nine months' time, but he is the favourite right now."
Nadal triumphed at Roland Garros in 2020 but has only appeared at two majors since, while Federer – who hopes to return to tour-level action in 2022 – last collected a grand slam title at the Australian Open in 2018.
Nadal is glad that the likes of Stefanos Tsitsipas, Alexander Zverev and Medvedev, who only dropped one set across the entire tournament as he denied Djokovic the perfect year, are taking over.
"They are no longer the Next Gen, we do not have to make it eternal," Nadal said of the new 'Big Three' in tennis.
"Players like Medvedev, Zverev or Tsitsipas have already passed that stage of the Next Gen, they are the current generation, the present."