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CCD technology was better several years ago but in the meantime CMOS has taken over (the difference is not that great though). Hence you have to check the date of the articles comparing the technologies. Most of manufacturers (including Nikon) are slowly migrating to CMOS.
Also I remember reading somewhere (a while ago) that the original Canon IR filter had higher transmission for H-alpha wavelengths and hence unmodded Canon camera was better suited for astrophotography. I don't remember seing a replacement IR filter for Nikon anywhere...
Basically, the choice is simple, if you don't have a DSLR, go with Canon. If you already have a complete system of lenses based on Nikon, stick with Nikon unless you have money to spare...
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