I had an 03 ninja and for some reason I remember the Ninja being quicker, but this was long ago, it was my first bike, and I was like 15 lbs lighter so maybe that's why. The top speed on the ninja was for sure higher though. I was able to get it to 95 at least and 114 once downhill. Ninja also sounded zippier if that makes sense, probably because of the extra cylinder.
Either way, both fun bikes.