The Treksters in San Francisco from ‘Star Trek IV: The Voyage Home’ (1986) my vote for the best Star Trek flick. The green building in the background is owned by Francis Ford Coppola, who runs his movie empire from here.
San Francisco Film Locations Then & Now
A Then and Now Tour and History of San Francisco Through Films and Photography
San Francisco Film Locations Then & Now 
I agree; yes, the best flick of Star Trek!