Synthesia is a commonly reported property of some psychedelics. Now, with Bear, he was an audio engineer and probably had a pretty good understanding of resonance. If you look at the bass speakers behind Mike Gordon of Phish (there are lots of high quality live videos taken recently) you can see that when he plays low notes, the metal grill on the speakers vibrates visibly. You can also see that even when damped, any video camera clamped to the music stage is vibrating from drum impacts.

I could easly see Bear, on Bear acid, at a Dead show, thinking "I can see sound waves" by watching something resonate in time to the music. I'm not sure but maybe some folks have seen actual notes flying out of a guitar, but that would be a very strong hallucination.