Another +1 for Albany Aquarium, it's probably my favorite shop in the area, really good healthy stock, and everyone I've talked to there seems pretty knowledgeable and is helpful. That place is ridiculously humid though. :/
Aqua Forest is worth stopping by, if nothing else, they have some really beautiful display tanks, and they have a pretty big selection of plants. That's also not a bad area to spend a bit of time, a bunch of nice shops, places to eat, etc. right around there.
I also like the Ocean Aquarium on Cedar, it's cluttered and packed to the ceiling, but the people there are friendly and helpful, and all the tanks look healthy, and are full of plants... The neighborhood can be a bit sketchy, especially if you aren't used to urban areas, but it's not really dangerous, just don't leave anything in your car (I'd avoid the car altogether).
If you are looking for things to do, The Academy of Sciences up in Golden Gate Park is pretty neat, and they've got a really cool rainforest... ?thing? walk-in paludarium? Anyways, it's neat. Almost as humid as Albany Aquarium.
And they've got a decent aquarium set up as well.