If I were buying again today, I'd still probably buy Canon, as they seem to currently have the lead in terms of sensor technology, but that's really just personal opinion.
I've got to say that I think it could go either way, especially if you're only concerned with shooting UW and limiting your lens choices to Nikon or Canon. If Aquatica supports both, it's down to lens choice. You've removed the biggest problem I see with Canon, which is a lack of options for housing their cameras.
In defense of the 300D, the new Sigma 12-24 supposedly makes up for the gap that Nikon created with their 12-24. It may not be as good a lens in terms of performance, but it's at least an option.
If you're interested in long lenses down the road, Canon's lineup of super telephoto's is supposed to be the best available (300 / 400 / 500 / 600 IS), but those are lenses that cost multiple times what you'll spend on the body. There are also a few specialty lenses that you can only get with Canon like their MP-E lens, or the 3 TS lenses. But again, these are very specific lenses and have nothing to do with your choice for UW.
The flip side of the lens issue is that Canon doesn't have an equivalent to the 70-180 micro, which is a very cool lens by all rights. The closest thing in the Canon lineup is either the 70-200 f/4 which doesn't focus very close, or the 180mm macro which is pretty expensive and probably hard to house.
You'll definitely find more people on this board shooting with Nikon mounts than Canon, and as a result will probably get more mileage from their experience.
Another point is that I (personally) have a problem buying technology / cameras that are due for a replacement. The D100 has been out a while now, far longer than the 300d, and is about ready to be updated in theory.
Just to make it more confusing, why not an S2 Pro or a 10D? I think the Nikon is the last body in the class that I'd buy if I was doing it again. Having TTL would be great, so the S2 makes sense. And I don't think I'd choose the 300d over the 10D, unless the cost is a significant issue.
Ok, I'm done rambling. Sorry if this made it worse... 
Tom