Nick Fury portrayed as black in Marvel's Ultimate universe, where he was seen as early as 2001. You can find the information and appearances here. The Wikipedia entry even notes
Nick Fury was redesigned to look like actor Samuel L. Jackson with his permission, who went on to portray Fury in several Marvel movies.
So Nick Fury as an African-American predates the first Iron Man movie by around 7 years.
However, the Nick Fury outside of the Ultimate universe and the movies is still generally depicted as white. This is the Marvel universe that has been going for around 50 years and sees Fury as a WWII vet. Ironically, in the universe where Fury is white, it has been revealed that he has a black son named Marcus Johnson that also looks like Sam Jackson.
This means that you'll see Nick Fury as either white or black depending on what universe you're looking at. I would also expect that as a branding tool you'll see more spinoffs created in which Fury looks like Samuel L. Jackson. In order to sell consumers the comics, Marvel will probably start drawing characters closer to how they're depicted in the movies.