Try to have the HDD turned on, but not attached to the case, that way you see if it's the harddrive itself vibrating, or just making a noise from within itself.
If it's vibrating, you should try and dress the sides with thin rubber stripes, so it doesn't have direct contact with the HDD rack, that way vibrations won't transfer into the case.
If it's teh HDD itself making the noise, you'll have to get a new HDD, or simply live with it.