I don't own a Nikon so only going off 2nd hand information, but from those that have owned both, the Canon appears to have less noise and is therefore more suited to astrophotography.
There are some people doing brilliant things with Nikons though, so it can be done.
But i've seen owners of Nikons for terrestrial imaging, get a cooled modified Canon for astrophotography. So I guess that says something.
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