(disclaimer)I have not owned both. (Actually, although I shoot Nikons, I will confess to having a Canon Digital Elph in the glovebox)
Anyone can make a line-by-line assessment, and trumpet that their brand is better. However, Canon, Nikon, choose either, and you'll be happy; either way you'll feel that you got your money's worth.
That was the short version. Here's the long-winded explanation:
Nikon makes great glass (lenses); Canon makes great glass. The bodies are both well built and the feature sets are pretty similar. Performance is pretty similar, too. I know some will jump on this last statement, but it's true. Both have strengths and weaknesses, and usually the performance difference is miniscule.
Part of my paycheck comes from journalism. Out of all of us, two shoot with Canon, the rest, Nikon. Here's my take on watching their cameras perform:
>Our Nikons take a beating. Their Canons take a beating.
>Our Nikkor glass is unhumanly tack sharp. And expensive. Their Canon glass is tack sharp, and just as expensive.
>The reliability of my Nikons was (and is) astonishing. Their Canons fail just as often, which is to say hardly ever.
>NPS makes sure I always have a camera. So does Canon.
>Nikon parts and techs are everywhere. Canon parts and techs are a blight on the landscape.
I have shot Nikon pretty much forever. The controls and human interface are perfect for me. For the next guy, it may be terrible. So this is a personal thing, and much more important in getting "the shot" than some meaningless tenth of a percent advantage in noise.... and only you can tell which one's ergonomics is right for you.
There are many excellent reasons to pick a brand. Housing availability, TTL compatibility with strobes, etc. Price. My personal recommendation is to work backwards, i.e. pick the lens first, then the body; fit the port to the lens, and the housing comes along with the port.
Honestly, it's truly almost a dead tie. If you don't have an investment in either brand, you'll be happy either way.
All the best, James