If you mean "Black" as in "belonging to an ethnic group from Sub-Saharan Africa" than it would have to be Doc Louis from Punch-Out since he's pretty likeable (and I hardly play video games set in the "real world" more or less, so there usually isn't an "Africa" for people to be from)
If you mean "Black" to mean people with darker skin tones I would probably have to go with the mechanic from Skyward Sword (I always looked forward to visiting him, his attitude just put a smile on my face) Basileo (spelling?) from Fire Emblem Awakening was also pretty cool
I actually hate Twilight Princess Ganondorf since the Gerudo are brown and seem to be based off of the Middle East inspiration-wise, but then in TP they decide "Oh Ganon needs to look evil so.... just make his skin a ton darker!" If Ganondorf getting demon-powers changes his skin color to be black instead of brown... uh the terrible things you could read into it.
Pokemon has gotten really good at putting lots of diversity in its games.
I thought it might have been something they would just do with Unova since it was based on America. But Kalos has a lot of black or brown people, too.
I took a trip to France and there is actually a lot more Africans than you would think. Currently there is a lot of immigration from France's former African colonies (mostly because they already speak French because of past imperialism and France is having problems with declining birth rates and is encouraging it)