Is this a problem that developed over time, or did it always do it?
Speaker hum in vehicles is very often caused by ground loop issues, in which there are multiple return paths to ground. This is often caused by using shielded audio wire and grounding the shield on both ends, which should never be done. There is a lot of nonsense about grounding practices floating around the Net, and I doubt that upfitters are immune.
One easy way to address ground loop issues is to get an isolation transformer, such as this: