My Guinea Pig Is Making Horrible Breathing Nosies. Can You Help?

I would ask if they have done a thorough oral cavity exam.  Guinea pigs can develop tooth root abscesses--the roots of some teeth are very close to the nasal cavity and can cause upper respiratory-like signs.  Depending upon the area of the country fungal infection may be a concern.  The nasal discharge can be cultured for specific bacteria and/or fungi.
There are veterinarians that specialize in exotics--have your veterinarian refer you to one.  They see more exotic cases and may have more experience with uncommon diseases seen in guinea pigs.

AS I said in a response before, it could be the bedding. MANY  wood shaving bedding give off dust and this fine dust (like microscopic splinters) get into their nose, throat, and lungs. Try a compressed pellet bedding made from newspapers or newspapers & hay ( Be aware he will eat some of the hay which is OK, but also may shred the newspaper  and the ink may stain his/her light fur  AND.make sure ink is non-toxic)... Sounds like you already tried the vet...give this a try .  I hope this works..