As mentioned before, Kingpin on the MTV Spider-Man series was black, in keeping with his appearance in the Daredevil movie. (By contrast, I'm not sure what race he traditionally is.)
He's not strictly a supervillain, but Scarecrow had a thug in Batman: The Animated Series known only as "Torchy" (he had a nifty drill/torch attachment on his wrist) who got more focus than most henchmen. There was also a particular henchman who seemed to keep getting bounced from boss to boss or something - black, wearing sunglasses and a goatee. I swear, it was the same guy, and I saw him at least three different times.