The raven boss (Raphael the Raven) in Yoshis Island. You fight him on the moon. 

The ones that I can think of immediately all come from the Punch Out!! series:  Doc Louis, Mr. Sandman, Mike Tyson,....

Also, I always thought of Urbosa as being from someplace like India.  Maybe that's just me.

Urbosa is not black. Urbosa is Gerudo and Gerudo are inspired the middle eastern cultures.
Vandham is not black either.

Twintelle is not only Nintendo's best black character but one of the absolute best black characters ever created.

Anthony Higgs - Metroid Other M

well since...bayonetta is mostly nintendo nowadays... rodin :P

Doc Louis
Kirby Sometimes
Yoshi Sometimes
Mega Charizard X
John Henry (Codename S.T.E.A.M)
Michael Edwards (Eternal Darkness)
Mr. Game and Watch

Oh, also Mr. Sandman:

You do known that when ask about "black characters" that everybody will assume people of African descent (especially in the west). I don't think you understand what your asking. If you meant Dark skinned then fine, but you didnt ask that.

Urbosa is not suppose to be a black person. The Gerudo are the equivalent to middle eastern people in the Zelda world. I would like to ask you - Is Jasmine from Aladdin black?

Vandham is not black man, Dark skinned fine. 

Not sure what mean when you say they are suppose to be black people....?.......... but I'm sure it does not make them black....whatever it is.

Why limit it to Nintendo tho? 
Several Pokemon characters like Nessa and Kiawe are the first that come to mind, but the most memorable is Olivia for me. I guess ill throw in Mike Tyson as well, since i have a soft spot for Punch Out. I cant think of many more that stand out or that I'd consider "the best". 

Whats that supposed to mean?

Incredible design. Nintendo has very few black characters, but when it was time to make another one they blew it out the water ....... I love her.