New Yorker but been living in SF for 6 years. Cellarmaker and Toronado are a must!
Breweries / Bars Grouped by area:
SOMA/Market:
*Cellarmaker Brewing Co* favorite brewery of all time, their hoppy beer kills, also their higher abv dark beers are legend ie, Coffee and Cigarettes
http://www.cellarmakerbrewing.com
City Beer Store, one block from Cellarmaker, great bottle shop with to go or drink on premise and like 10 rotating taps
http://citybeerstore.com
Mikkeller Bar, little bit of a walk to market from the last two, but great bar with bottle sours and guest taps, food is good but pricey
http://www.mikkellerbar.com
Nob Hill area:
Liquid Gold, newer bottle shop and bar with 20 taps
http://www.liquidgoldsf.com
Hop Water Distribution, bar with decent food, 30 taps all California made beers
http://www.hopwaterdistribution.com
Haight:
*Toronado* favorite bar in SF, they always have draft Pliny/Blind Pig on tap, the place is legend in the Bay Area beer scene, also do yourself a favor and grab a Rosemundo next door to eat inside Toronado
Black Sands, few blocks from Toronado new homebrew shop, brewery, bar, I like this place it's only been around for a year, they normally have 3 beers on tap with guest beers in bottles, they also have a small food list
http://www.blacksandsbeer.com
Mission:
Monks Kettle, high end food, great bottle and draft selection, everything here is incredible, best slow dinner craft beer place
http://monkskettle.com
Zeitgeist, it's a bit of a walk back towards Market, great outdoor space in back with picnick tables, lots of taps, burgers and fries grilled outside
East Bay: (across the bay bridge / ferry / bart train)
If you want to leave the city, would recommend taking the Ferry across the bay to Alameda (awesome views and ride) then walking to Faction Brewing
http://factionbrewing.com (everything they make is awesome), from there you can Lyft/Uber up to Berkeley to hit up Fieldwork
http://fieldworkbrewing.com (newer brewery with many taps killing almost every style of beer) from Fieldwork you could Lyft/Uber back to SF or take BART back. Bonus great bars in between Alameda and Berkeley in Oakland, The Trappist and Beer Revolution.
In a galaxy far far away...
Everyone will prob tell you to make the trek up to Russian River and Laguntias, unless you have a DD its not worth it, it's a decent drive, will take up a whole day, but the above places are all in SF grouped by walkability once your in that neighborhood. I would recommend lyft/uber to hop around to neighborhoods then walking.
Cheers!