Eliminating the noise at the source is the best course of action.

The various filter gadgets available are just band-aid solutions in my opinion.

Because the problem is only present when the engine's running it's probably either alternator whine or ignition noise.

You could disconnect the alternator and just run off of the battery for a bit to eliminate the former.

Ignition noise usually means that resistor wires and sparkplugs are on the agenda.

Earl