That figures. It's hardly ever the easy stuff.
Are we still talking about the stock head unit? I noticed you said you have an amp for your sub, so is it safe to assume there's an aftermarket head unit too? A good ground strap/connection for the head unit never hurts.
As far as the sub amp goes, is there any type of noise suppression on the power feed for the amp? Inductive interference caused by speaker wires running too close or parallel to power leads can cause radio noise, so a noise suppressor on the power feed near the amp, or re-routing speaker wires or power leads (whichever is easiest) can sometimes cure the problem.