You should not want to switch to Canon because your autofocus speed is too slow. That's very much camera and lens dependent and you can get fast autofocus with Nikon. You certainly shouldn't be considering the current 5D if autofocus is your top priority.
With Nikon, choose only AF-S or similar macro lenses and a housing that supports the back focus option. There is a lens at every focal length that will do that, so Nikon doesn't have to be any worse (or different) than Canon in that regard. For wide it doesn't matter so much. A D300, D700, or D3 with the right housing and right lenses will address your AF concerns.
If switching to Canon is what you want, this moment is probably not the right time. The new 50D looks good on paper but isn't available yet. The 5D replacement is expected soon. The 1Ds3 is a very pricey choice if you feel the need to be impatient.
People argue Canon and Nikon and I think it's mostly pointless, but it's entirely pointless underwater. You don't shoot a brand underwater, you shoot and entire rig. The greatest body ergonomics in the world don't matter when it's a housing that you are handling. Fortunately, both brands are supported well, but you need to choose an entire system, not one component in a vacuum.