Always seems weird to me that tourists associate this with SF, but I guess it started at the Wharf in the 90s, so they all saw it and locals didn't.
Earliest mention I can find of this dish is from a 1984 San Diego tourist guide, which refers to O.B. Pier Cafe's "famous clam chowder served in a bread bowl."
It was in Arizona and New England before the first reference to it in SF, in a 1992 guidebook, which doesn't say where you could get it. A 1995 guidebook says "the corner of Jefferson and Taylor is jam-packed with street stands that hawk all kinds of goodies, including ... thick clam chowder in a bread bowl." First reference I find to it specifically at Boudin is 1996.