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I can't comment on Nikons as I have never used one. But in this day and age, surely the difference between the 2 is negligible and comes down to pixel peeping.
My only comment would be that since getting the Canon 40D, the liveview feature and additional capabilities of shooting while connected to a computer are far better than the Canon 30D. So, if I was going to buy either Canon or Nikon for astrophotography, I'd be looking into it's capabilities of shooting through a computer - liveview, can you do longer exposures than 30s, and so on.
And might also depend on what capture software you're going to use. I've seen Canon cameras as an option in Nebulosity for example, but don't recall seeing the Nikons. Just something else to consider. Make sure your capture software will work with it.
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