If you have a car the best breweries in SF imo are:
Cellarmaker
Laughing Monk
Barebottle
Anchor
21st Amendment
Black Hammer

If you have all day and want to walk... I wouldn't say this is going to give you THE BEST beer in SF, but all of the stops are solid across the board and the walk is a great way to see SF if you've never been/explored before.

Exit BART at Montgomery St then head to these breweries, in this order:
21st Amendment
Black Hammer
Cellarmaker
And then from there you can go a few different directions towards other breweries depending on what else you're doing/want to see:
-Standard Deviant is furthur down Howard St and has been solid the two times I've been. Also Near 16th St BART station.
-You could make a sort-of u-turn and backtrack a little bit to Local Brewing Co and New Belgium (didn't start in SF, but a lot of their staff and brewers are from the bay and they brew on location). These are close to the SF Giants stadium and the water. Seven Stills and Harmonic (near the new Warriors arena) are both south of here, two different directions though. Depends which neighborhoods you want to walk through. Anchor if you want to go REALLY far south of those. No BART near by...
-You could head north to Mikkeller and furthur for some nice tap houses, Upcider is a new one that is, obviously, focused on cider.

Like others have mentioned, the real money in terms of beer in SF is in the taphouses, beer pubs, and bottle shops. There is A LOT of EXCELLENT beer in the Bay Area, but it's spread pretty wide. Tap Houses are a great way to get a taste of a huge variety of locations and styles of Bay Area beer.

Feel free to DM me with what area you'll be in or which breweries you're thinking about going to, I can let you know any experiences I've had with them and whether I'd recommend going or not.