I'm not a Nikon guy, so I can't say that you'll be okay with 100% certainty, but I'm sure there would be some pretty loud rumbles around here if Aperture didn't recognize RAW images from one of the most ubiquitous DSLRs to date.
Aperture, Lightroom, NX, etc. will all convert D40 RAWs. Which one you like best is up for debate--each program interprets the RAW file slightly differently.
I prefer Nikon Capture NX2 for RAW because I think it does a better job, but any of those other programs mentioned will work just fine with the other files.