Wait, no disregard that I suck cocks. Had one in my mouth right then while pausing for dramatic effect and I'm still not as big a faggot as you.
Exploration of Sub-Saharan Africa began in the 15th century. They actually called it the Age of Exploration. Ironically not because they didn't know about Africa or black people, but because the interior of sub-saharan Africa had yet to be thoroughly explored and only the Muslim conquest of Sudan that opened it up. You ever see a Sudanese person? Getting pretty dark.
There had been Arab slaving going on since pretty much forever, but it really kicked into gear with Islam. The kingdom of Nubia, named for the Noba people who migrated there in 4th century BC and are the current ethnic majority, was actually a Christian Kingdom. It survived all that time to the present even, although it's now called Ethiopia.
So the Muslim Caliphates were interacting and enslaving Africans for centuries. But would they sell to central Europe?
Let's talk about Wallachia. You know, part of Romania now with Transylvania and Moldovia. Wallachia came under the control of the Pechenegs, a swarthy people known for worshiping Islam and being Turkish.
So yeah, it's concievable that during the location and time in real life that Innistrad is based on, not just Africans but Negroids from African kingdoms could have been present there.
All of this is ignoring explorers, envoys, adventurers of circumstance or wealth, preachers and religious pilgrims seeking truths in distant places that have always popped up randomly.
No, there never were any significant or established Negroid communities or colonies that I know of. But there were individuals present, and the place you would see them would be at courts as a novelty, or because of their exceptional or unique skills, or in mercenary bands, or with goods to trade, or being entertained by the Church as pilgrims, or argue with as heathens, or to get them to accept missionaries etc.