Low Subwoofer frequencies often generate a considerable amount of rattle when played at high volumes in cars. The best way to eliminate rattling is to use a sound dampening material to absorb the soundwaves created by the subwoofer before they can reverberate and rattle parts in your vehicle. Sound dampening material is an adhesive material that can be stuck to the inside of doors, the headliner, the trunk or anywhere else a rattle can be heard.
Here are a few types available on Amazon:
2) Noico 80 Mil
10) HushMat 10200
I have not included prices because they change all the time :)