I know how much of an annoyance this can be and how much of a pian it can be to isolate the problem.
try this, start the car turn the radio on where the noise can be heard then disconect the alt wires just the plug in and see if it goes away. If the noise goes away when the alt is disconected the you can guarente thats the problem. The loom inside the alternator is loose or a diode is failing.
You could replace the alternator but it might not fix the problem entirely. You might want to tray a cheap noise filter. Scoshie<-- I belevive is the cheapest, "wall mart Kmart" and they seem to work well.
If the noise doesent go away then its the actual stereo equiptment and becomes complicated to chase down the problem as you know