I recently bought an Eye-Fi Pro Card. A nice little gadget for my camera(s). The Pro version has - among other features - RAW support and geotagging pictures, but unfortunately not both together. It does geotag JPEGs via Skyhook's WIFI Positioning, which works reasonably well (in Zurich City at least) and is better than nothing, but certainly no GPS replacement. It also does upload the RAW pictures to my computer (even if it is offline, they get downloaded later from the eye-fi server). But it does not geotag RAW pictures, something I knew Aperture can handle with Nikon's NEF format. I found this this forum entry, but just to find out, that others have the same problem. So I went and did my own solution.
My Nikon D90 can save JPEG and RAW simultaneously and that was the way to go. I set the camera to store JPEGs as Small and Basic Quality, so they only take up approx. 200kB. Then later, when the pictures are on my computer, I wrote a little script, which reads the geoinfo from the JPEG, looks for a similar named NEF file and put the geoinfo in there. For that I used Exiv2, which handles NEF perfectly fine. After geotagging the NEF, I move the JPEG to some other directory for later removal and import it into Aperture. So I only use the JPEG for transporting the geoinfo to my computer and to the NEFs and I don't have to store them "forever".
The script is at Github, it's very basic. My bash foo isn't that good, forks and improvements are very welcome.
BTW, if you're importing JPEG and RAW into Aperture anyway, that's all not needed, Aperture should handle the metadata good enough in that case.