A filter is a bandaide, solving the actual problem is a better solution. Bbut yes, this is generally what is called alternator whine.
If the ground on the amp is okay, here's what else I would check. Is the amp itself mounted to metal? It shouldn't be. Have you tried messing with the ground on the h/u?
If all else fails, fall back on the standard troubleshooting method in car audio: isolating components until the problem disappears. Do you have a boom box/portable radio that has RCA output jacks? Hook it into the stereo, bypassing the h/u, and see if the problem is still there. if so, move on to the RCA cables. Putting the h/u back into the system (not the portable radio), run a temporary rca cable over the seats and back to the amp... is the problem still there? If so, you know the problem is in the amplifier (or its installation). If you have any other components in your signal chain (like an EQ, line driver, etc) use the same methods to isolate it by removing it from the system and find out if the problem persists. But remember, the key is to isolate/remove only one component at a time... this includes wires any/or cables.
Hope this helps.