Have you tried mounting the power supply in a metal box and grounding the box / tube? ( Faraday cage ) You might be getting noise from radiation not conduction. Have you tried a hand held radio in the car to confirm the noise is coming through the power lines?

Next, the block diagram won't filter noise reflecting back into the 12 V supply only noise moving forward on the 5 VDC line.

How much power do you want to use? You can try a LM7805 regulator chip, these burn off excess power into heat so you will need a decent heat sink. These should make a reasonable clean signal with a capacitor on the output. The LM78xx series can be has in various stock voltages and there are adjustable versions / negative side regulators as well