Depends on what lens and what you are using it for, and what year is it is ( ie; models.)
If you want to use off camera flash the I feel Nikon is the way to go because of Nikons CLS lighting system.
However when I am shooting motor sport with my Canon 100-400 F4.5-F5.6 IS L, Nikon owners say to me "I wish Nikon made a lens like that" and I think "his camera may focus faster and more accurately than mine than mine".
At the end of the day it is a system that meets all your needs.
If you have a fair investment in Lenses then stick with the brand you have now if not then from purely a numbers point of view you may want to check out DPR especially their camera comparison.
Buying Guide: Side-by-side: Digital Photography Review