The camera will display the image based on your existing picture control settings, but these settings don't specifically mean anything when dealing with the NEF after the fact. Lightroom has some presets (I don't use Aperture, so I can't speak to it) for raw development that apply a "start point" that are quite similar to the picture controls, but are not quite the same. The View NX2 software supplied by Nikon will use the picture control settings from the camera as the information about your current camera settings are stored in the image file, but you can still adjust from there.

Bear in mind that every time you display the NEF, something has to interpret that raw sensor data into an image (unless it uses the embedded JPG). How it does that depends very much on the application doing the work. The camera and NX2 are going to be fairly similar, other applications will vary.

Also, make sure your display is calibrated. That's pretty important as the image may appear worse than it actually is.