Rafael Nadal's picture isn't next to dictionary.com's definition of "dominant," but probably should be.
The word is defined as "ruling, governing, or controlling; having or exerting authority; occupying or being in a commanding or elevated position; main; major; chief."
Notice that each and every one of those explanations is firmly rooted in the present. There is no mention of past history, merely what is happening in the present. For that reason, Nadal can be the most dominant player in the game without being the greatest in a historical sense.
Consider this football metaphor. In 2001, Drew Bledsoe was the New England Patriots' franchise quarterback and unheralded second-year Tom Brady was simply riding the pine. When Mo Lewis essentially ended Bledsoe's career with his bone-crunching hit, Brady was thrust into the starting lineup and led the Patriots to the Super Bowl.
Brady quickly became the most dominant player at his position, but at the time, Bledsoe had more historical success. Therefore, Bledsoe was more historically great, but Brady was more dominant at the time. That would quickly change, but that's irrelevant here.
This metaphor holds true for the story of Roger Federer and Rafael Nadal.
There is no debate about who is the greater player in a historical sense. Federer, the holder of myriad records including the coveted Grand Slam title record, blows Nadal out of the water.