You should be able to leave VR on but turn it off to make sure it's not the problem.
OK. I just used my D5100 and AFS 18-55mm lens to take a movie. If I am very close the way you are my camera/lens makes the same noise as yours when the scene is not in focus. It's hunting. It won't chatter like that if you use manual focus or in AF if you make a movie at a reasonable distance from the object and keep the scene in focus. It will take some practice. Also since your built in mic is so close to your lens it's picking up and magnifying the noise.
There is nothing wrong with your camera or lens just your technique.