I can't say, as I don't own a Nikon and have never used Nikon Capture.
I find Aperture's noise reduction "okay," but that's mainly because my 1D mark II has pretty good performance, even at ISO 1600, for images that are properly exposed.
I will say, though, that for images where I really want to do some noise work, that I just open files in Photoshop and use Noise Ninja. Noise Ninja is very, very good, and with Aperture's integration with Photoshop this is workable for me. I tend to not do NR on may images -- just ones I'm going to publish or print.
Are you frequently shooting indoor sports?