The sad and plain truth is that there is definitely better support for Canon cameras in astrophotography circles. Canon are not "better" cameras overall - far from it - they are merely an alternative that seem to have some small traits that suit astro work better. Current NEF (Nikon's RAW) image format is pre-processed - i.e. not entirely raw as such - where the Canons' are. The new Nikon firmware in the D300 and D3, I believe, now supports a true RAW image, but I need to check on that.
I far prefer the colour and tonal qualities of Nikon cameras that I've used over Canons that I've used for terrestrial duties - but that's me. Others will disagree. I also way prefer the feel of Nikon bodies - they suit my hands far better and feel far less "cheap" in the hand. I also prefer the menu systems - far more logical than Canon menus - again - to me.
Canon have third party manufacturers such as FotoSharp and others supporting them and not Nikon users. Go figure.
The new D3 (uber-expensive) and D300 are starting to make inroads now though. My D40 (CCD) has very low noise and amp glow characteristics (far lower than the previous D50 & D70's), but the D300 is lower still and has taken on CMOS as its underlying technology now too. High ISO performance of the D3/D300 is reputedly far better than that of its competitors - but the leap frog effect will come into play soon no doubt. I think that people put far too much value on a high pixel count. Higher number of pixels does not equate directly to "better" quality images - it's up to interpolative software to manage the resources and image quality produced. In fact - it's been touted by many that as pixel density increases on the array, the noise levels increase as a direct consequence - which is why Nikon did not push the D3 beyond 12Mp - to their credit. The D3's high ISO performance is testament to this.
There are plenty of people that use Nikons for astro work Steve. Just go to Cloudy Nights to see that - but if you just want to go with the "flow" and not argue with anyone - go Canon. I never thought I'd say that. LOL! If I didn't have over a dozen Nikkor lenses from a family of Nikon users 'd probably do a Canon 5d. For reference, Shevill Mathers from Tasmania is currently using his Nikon D100, D200 and D300's to great effect.
At the end of the day Steve - I'm a loyal Nikon user because my old man let me use his Nikon F (the original and very first pro SLR) back in the early 70's - as well as his El and EL2 bodies and raft of lenses. The F has done well over a million frames in its life - and it still looks and works like new. They have all been utterly reliable for nearly 40 years - and were used extensively because my father was the president of a large Sydney camera club for years. On the flip side, I had a Canon T70 and original EOS film cameras back in the 80's (rebelling against my father for some reason) and a couple of Elph digitals is 2002-4, and they ALL broke or failed for various reasons - none have survived the easy life I gave them. There' my reasoning.