Aperture does not support D700 NEF (RAW) images yet. Aperture has been notoriously slow about picking up RAW support for Nikon cameras (and maybe other brands also) in the past. The same problem existed when the D200 came out, and again when the D3 and D300 were introduced.
I have been simply shooting in RAW + Large Fine JPEGS and then importing the JPEGs into Aperture. This works fine and gives plenty of quality for most situations. In fact, I do a lot of low light shooting at events and I don't believe Aperture does justice to the low light capabilities of the D3. So I have been using JPEGs from the D3 to import into Aperture whenever I am shooting at high ISO settings.
I like the Aperture workflow, so using the JPEGs gives me the benefits of that workflow and still results in good image quality. So that is why I use this work around.
I can always go back and convert the NEF file in Capture NX2 if I don't like the results for some of the images - but I rarely find this necessary.