Aquatic Collection in Hayward is my favorite LFS right now. It's on the way home from work for me so I stop by there every so often. The coral selection is probably the best in the area (gotta be most gallons), best prices I've seen and they get some really nice livestock. Great guys too. They buy frags!!! which helps subsidize my habit a little. TBH on the minus side their fish sometimes don't look too healthy & I've noticed aptasia in their tanks. But then I've seen aptasia in most LFS, so....
The other place I frequent is
Ultimate Aquarium in San Mateo because it's the closest to home. I buy consumables here (phyto, food, etc.). Sometimes I get lucky & they have something cool, most of the time they got nothin'. But I like the staff so I give em props for being helpful & friendly. They do have a decent selection of fish but honestly I am hesitant about buying anything from the side tanks. The side tanks are all connected & turnover is high so I'm worried about disease. Always quarantine! Back tanks are better, they put the best (expensive) livestock in the back. I only mention this place because I got my Purple Tang & elegance coral here, 2 of my favorites & I paid a reasonable price. If you're a regular you can haggle with them. Again, very hit & miss; depends alot on when you go. They don't buy frags.
The San Carlos/Belmont place is called
Aqua Exotic, & they still don't have a storefront AFAIK. You have to set up an appointment, but I recommend doing so if you're in the area. The livestock looks really good & prices are generally reasonable. Selection is limited right now, but when I went it was in an apartment. I'm really looking forward to this place opening up 'cause it's SO CLOSE!!!!
I've also been to
Neptune and I think it's a really good LFS if a bit on the expensive side. It's a little off my usual beaten path, so I don't get to go down there very often. Livestock looks really healthy & staff was great IME. They have some really interesting SPS.