First, you may wonder why only the choice between two manufacturers? After all, Sony, Olympus, Panasonic, Pentax and Sigma all make DSLRs. The answer is simple: these are not professional manufacturers. Maybe they were, once upon a time, but not now. Even Nikon had fallen from professional grace for a decade or more and is just now recovering.
So, Nikon vs. Canon?
|Nikon D3 vs. Canon 1DS Mk3|
I myself shoot Nikon. My choice was largely made for me; when I was learning to be a photographer, my mentor shot Nikon, and it didn't make any sense for me to be shooting Canon when he had so much experience with Nikon. So Nikon is what I bought.
There are not a lot of differences between the two manufacturers. Both of them have been at this game, building camera bodies and lenses for decades longer than I've been alive. They're both phenomenal at it, too: there are Nikon lenses good enough that Canon users buy adapters to mount them on Canon bodies (vice versa is not possible because the Canon lens mount is larger than the Nikon, so they just won't fit, regrettably).
|EOS to F-Mount Adapter|
As with many other competing companies, Nikon and Canon tend to leapfrog each other with regard to who has the better camera. They also largely have the same developments regarding optics; there are some Nikon lenses that Canon hasn't replicated yet, and some Canon lenses that Nikon hasn't worked out on their end.
So this is really up to personal preference. Certainly if you have any money vested it does not make sense to sell all that and start over. Once you pick one manufacturer, stick with it.