Ryan, a question:
You do realize that PM is not a RAW convertor? It can either only exctract the emedded JPEG preview inside the NEF (which is around maximum 1MB in size and pretty high compression in most Nikon cameras), or it can rely on Apple's own RAW conversion built-in to OS X (whcih does colours quite differently to camera). If you nevertheless want to just exctract the previews (which might be fine for small photos on web or emailing previews), you can give it a shot. Just understand that the files produced will be low-quality embedded previews produced by the camera, so you could just as well shoot RAW+JPEG...(and probably get better results). PM allows all operations on RAW+JPEG photo pairs very well, either as on a pair or separately.
Also, you have posted two photos which makes it hard to tell. From a quick look, what is the colour space your camera is set to? AdobeRGB? sRGB? And especially as you combined them together to one photo with undefined (or your monitor's) colour space "ColorLCD" (is that Apple's default for macbooks?), it's very hard to tell anything more where could be the problem. But I am betting on colour management mishap in your settings.