You pose a very general question, without giving any hints about what would suit this person. San Francisco has all kinds of shopping experiences available to someone who wants to stay out of the big chain stores. Most of those, incidentally are in the Union Square area and adjoining Market Street by Powell Street.

Maybe the thing to do is to explore the commercial blocks of Hayes Street, or Union Street, or Valencia in the Mission. If your brother-in-law is youngish, maybe somewhere on Haight.