Unless you get a shitty lens, they are pretty much the same. I mean, one or the other probably wont ruin the work, just will need to put some extra effort to bring it out later.
Just like insmac said, the differences are real. Nikon is usually sharper then Canon and I haven't seen anything that tops Zeiss on an FF body. But when it comes down to the final results, having an image from a top quality lens just makes it a bit quicker to get to there, like having no need to correct CA, vignetting and distortions.