Most likely problem is the amp's ground wire or ground point. The ground wire should be big enough to handle the amps your pushing through it. 1000W amplifier could be drawing as much as 83 amps. I would use 4 AWG. Anything smaller than that could cause your noise.

The ground point should be close to the amp and a good ground source. Make sure you have metal to metal contact over the entire surface of your ground connector. Clean it up with a wire brush and coat with a dielectric grease to prevent corrosion.

Hope that helps