If you're looking for a great bottle shop, check out Olive Tree in Ocean Beach. It's about 10 minutes from your hotel, located on Sunset Cliffs, and has a killer selection. You won't be disappointed. Most of the others mentioned are bars, some being pretty cool.
I'd agree with the Ugly. I have a growler of it in my fridge. Outstanding example. Better than the Sublimely Self Righteous or the one from Deschutes in my humble estimation.
Not even a shout out to one of the finest the world over, Speedway Stout from Alesmith? I'd even, albeit a bit more reluctantly, throw Sea Monster from Ballast Point into the conversation.
A bit late to the game but what, no mention of one of the finest examples on the planet? Speedway Stout from Alesmith is easily one of the best. A 12% behemoth from one of the best breweries in the country.