Psychologically, Raphael is the stronger fighter… While his initial characterization is one of a rage-aholic, it is an anger that he does eventually learn to rein in, and even control as the various series progress. In the upper tier of combat, especially that involving life and death scenarios, mental strength and resolve is as much if not more important than weaponry, fighting techniques and experience.
Further, in the 2003 animated series, when Leonardo loses his self-confidence after being very badly beaten, Raphael is the one who nurses him back to health, and helps to restore at least some of his former confidence in himself. It's fairly clear that Leonardo carries along with the burden of leadership, a great deal of self-doubt, as well as a role of responsibility within the group that could both be exploited as weaknesses by a savvy opponent.
Raphael, by contrast, has little of either issue, and as a natural loner, is thus a better "pure fighter" – put both in the boxing ring unarmed, and I will put my life savings on Raphael every time.