It sounds like what you are hearing is the VR engaging when you half-press the shutter button, and then disengaging after the shot. To test this, turn off the VR on your lens and see if you still hear the click.
I have a similar experience with the 55-300 NIKKOR. Mine only makes the noise (clunk) when the VR mechanism is returning to the static position. There is a visible image shift in the viewfinder when it occurs.