In Fisherman’s Wharf proper, I second rec for Scoma’s. Yes, pricey, touristy, but the food and service has been fine-tuned and polished over many decades.
Sotto Mare is also a very good suggestion, a leisurely 20 minute walk, or a quick ride on the 30 Stockton. Our last meal at SM was about a month before the lockdown, best swordfish ever (imo). Actually, the Cioppino and everything else warrants a return visit. Soon.
One of our first post pandemic was at Portofino, an under the radar resto in North Beach. Portofino has been in operation since 1937, and seems to cater to a mostly local clientele. Comfortable heated parklet dining, as well as roomy comfortable indoor. Service was friendly and efficient.
Tender octopus, memorable.
1st Rockefeller in many years.
Roasted sardines.
Tasty fritto misto. Scratched my itch for fried fish.
Second Red’s Java House. Relaxed outdoor seating on the pier, beware of the thieving seagulls.
Pier 23 is also a nice spot for a beer (or three) and good fish n’ chips.
The Eagle Cafe on Pier 39 used to be a Fisherman’s diner in the day. Now a total tourist spot. One of the few places where you can slurp down some fresh briny clams on the half, washed down with a chilled bottle of Pinot Grigio.
Damn, the sun is shining. Might have to stroll down for some. 
