What is your setup? 60mm or 105mm lens, do you have a magnifying viewfinder? What Mode do you shoot in?
I shoot a D7000 with 105mm, and I have to shoot the lens in Manual focus. Leave the lens in A/M mode via the switch, and turn off the VR. My friend has the same setup as I do, but he has a magnifying viewfinder. The viewfinder helps a lot, but it comes down to your eye and where you place the focus plane.
If you are shooting in A, S, or P mode, get out of these mode and go to manual. I shoot only in Manual, shutter speed is either 1/250 or 1/320, aperture F10 or smaller aperture.