When you shoot a jpeg, the camera makes a series of decisions about your image for you -- how much sharpening to apply, the tone curve, the color space, how much noise reduction, etc. Shooting raw allows you to make these decisions at the time of processing.
Without a doubt, the proprietary Nikon software inside your camera (or in Nikon's raw developing software) will do a better job than LR.
That's why the jpeg will have less noise than the raw file -- no decisions have been made about the raw file -- it's just the raw data that comes off the ccd.
I don't know what settings in LR are best. If I have lots of noise to deal with, I edit in PS and use Noiseware to get rid of the noise.