Make sure that the drive mounting hardware (plastic slides) are properly seated on the drive, and make sure that they are fully inserted into the slot (you should hear a click when inserted).
If the drive is creating the vibration when properly seated, try removing the drive, and powering up the system just to verify. I have 4 hard drives, a DVD and BluRay player - no vibrations were detected on my system.
If it is the drive, there could be an alignment problem with the spindle causing the vibration - hard drives aren't silent, but they shouldn't emit loud vibrations...you might want to consider replacing the drive.