It could be as Steve said but I would try the following.
Try running the pump in your hand, not in the magnet holder and see if it is noisy running while you hold it. In this way you can determine whether it is the magnet holder vibrating or the actual pump that is noisy. If it is quiet than check the magnet holder.
The magnet holder should have the rubber feet installed, if the glass is thinner than 1/2" you may need an additional rubber pad. Make sure the magnet holder does not have any blisters or defects, raised portions which may be directly touching the glass. I have seen a couple where their were small bubbles in the potting resin that touched the glass.
If it is the pump. Open the pump and check for any foreign objects, make sure the front cover is on straight. The noise reduces substantially over the first 2 weeks as the parts wear in and seat.