If you are serious about macro photography, I would recommend buying a 'cheap' digital SLR and spending maybe 50% of that $1000 on a good macro lens. The truth is that these days even cheap digital SLR bodies are quite good (e.g., low noise, enough megapixels to make decent-sized prints). The limiting factors are often the lens and the operator (i.e., you). It doesn't make sense to buy a $1000 camera and use the kit lens for macro photography. You'll get much better results with a $500 camera and a $500 lens (not to mention that lenses depreciate much less rapidly than bodies, so you can always resell it if things don't work out).
In terms of Canon vs Nikon, at most price points, they are roughly equivalent, each with their own set of minor relative advantages. In other words, you can't go wrong with either.
That said, I know Canon better, so if you were to choose Canon, I would go with something like the Digital Rebel XS (with kit lens) along with a $400-500 macro lens like the Canon EF-S 60mm f/2.8 Macro USM or the Canon EF 100mm f/2.8 Macro USM (I own this last one and it's excellent). Make sure you get a kit lens (usually 18-55mm) so you can use it for general photography.
One plus-side of the steep depreciation on camera bodies is that you can save a few bucks by buying a used body. You can buy excellent used cameras for $500.
Get a super-cheap tripod too. It'll make a huge difference for macro photos.
Check out this page:
http://photo.net/learn/macro/
Here are user-submitted sample photos from the lenses I mentioned:
http://www.pbase.com/cameras/canon/ef_s_60_28_macro_usm
http://www.pbase.com/cameras/canon/ef_100_28_macro_u
Make sure you hit the "more" button.... each lens has thousands of submissions. I find that it's useful to see what kind of photos a particular lens (or camera) are capable of.
You can search by camera too:
http://www.pbase.com/cameras/canon/
http://www.pbase.com/cameras/nikon/
The main caveat with user-submitted photos is that the better photographers often (though definitely not always) have better equipment, so it tends to exaggerate the difference in quality. In other words, if the Canon XS photos look worse than the Canon 5D Mark II shots, it's not necessarily the equipment's fault....