Hopefully when you installed the alternator, you went with an OEM one as there have been plenty of issues with lots of the aftermarket alternators. Definitely replace the rubber dampers if they weren't done when alternator was replaced. There is a great chance that those are the source of your noise and replacing them could cure the problem. Not sure why the Honda dealer told you those weren't available. They are listed as available at most of the online parts places. Also that ebay info above is a listing by Cyclemax which is a well known place and good to go. The ebay link for those is
These are OEM Honda parts. They mount between the alternator and the engine. These will fit all Goldwing GL1500's from 1988-2000.
www.ebay.com
Or you could buy direct from them especially if there are other things you are considering for your bike.
Goldwing, GL1500, Alternator Dampeners, Honda, 13534-MN5-020
cyclemax.com
I prefer buying from them direct and have purchased many things from them in the past.