I think most alternators make a lot of radio frequency noise and it is not necessarily an indicator that something is wrong with the alternator.
The noise in your speakers could be RF noise, or a "ground loop."
Before messing with the alternator, I would try an RF filter on the 12v+ going into your stereo and amp; also make sure all of the audio components are grounded to the chassis.
Did the noise start after you installed some other electrical device that might not have a good connection to ground?
Basically, I think the noise in your speakers is a problem with the way your stereo (or some other component) is wired, not with your alternator.
You may well need a new alternator too, but I doubt that is going to fix the noise in your speakers.