Well, Nikon had the edge on flash up through 2012 so this has given Nikon the name in flash for a long time. So, perhaps now there’s not that much difference any more. Ken Rockwell has a bit to say about this under the section “Flash” in this article: http://www.kenrockwell.com/tech/nikon-vs-canon.htm
But they still are different. There’s a good list of the differences in the “Lighting” section in this article: http://betterfamilyphotos.blogspot.mx/2012/05/comparison-between-canon-and-nikon.html
The big thing for me is the inability for any Canon camera I have owned to trigger a speedlite off-camera, whereas I’ve seen Nikon folks do this. That was several years ago, so I’d be interested to know now which cameras on both sides support triggering speedlites off-camera.