Many think that Nikon cameras currently have better high ISO performance than equivelent Canon gear because of their Nikon spec'ed Sony made, image sensors.
Canon makes its own sensors, which to me is a plus. Sony sensors are nice, but they're still made by Sony.
As for high ISO noise, it's hard to compare. The D700 for example has a 12MP sensor whereas the Canon 5DMk2 has a 21MP sensor. Given the 5DMk2 has almost twice the resolution of the D700 its high ISO noise is about equal. That's VERY impressive. As you increase the pixel count/density high ISO performance generally takes a hit. Canon has pushed the 5DMk2 to new levels while keeping the high ISO performance exceptionally high, as high as anything Nikon makes.
I push my 5DMk2 to 6400 and beyond and am always impressed with the low noise. It's crazy to think you really don't have to worry about high ISO noise with it at all really. Even if you push things too far, the noise is so slight it's easily removed with software. Things have changed a lot in the digital camera space over the last few years.