Drew, excellent point. Alternators will generally whine anyway, but if one of the bridge diodes is open, this will defiantly aggravate the noise.
If your able to do like Drew recommend, i.e. isolate or disconnect the alternator, this would tell you if its an alternator problem. ALSO, If you can't isolate the alternator, try loading it up, i.e. turn on everything electrical, lights radios, etc. If the whine gets louder under load, then its definitely alternator.
An Alternator filter will help, but generally the filter capacity of the over the counter "Alternator Noise Filters" is nowhere near the filtering capacity of the smaller "individual filters".
You may not be able to get rid of the whine with the alternator filter, but keeping it out of the intercom and radio power supplies with the small individual filter should solve the problem.
Normally, in an automobile, the alternator and the battery are only a couple feet apart. Te battery itself acts as a giant capacitor to filter the noise. In our application, these are separated by 15 feet, so the alternator noise can generate a very small voltage in that 15 ft of wire, this is the the actual "source" of the noise you hear.
I'd do the shotgun approach. P lead filter, Inductive filter the radio and intercom power, and make sure the mike and audio lines are routed and terminated correctly.
Waiter