Well, the best one I know of was Flax, but they are moving to Oakland by 2/15 at
earliest. They have opened up a smaller store in Fort Mason, but I have yet to visit it and check out if they've carried over any of their ink/nib/paper supply to that location. If they haven't moved from their Market Street location by the time you're there (seems unlikely that they will), definitely consider going - the whole store is glorious!
www.flaxart.comOther than that, I know Bellocchio (
www.bellocchio.com/catalogue/papeterie/) has a lovely stationery selection, as well as some ink and nib offerings, but I can't speak for the extent of it since I refuse to let myself go in there - I've been told by friends that it will obliterate my bank account.
I hope there is someone here that can provide another option - I've been on the hunt! About a year ago I was told by someone at the art supply store that I usually go to in SF that "calligraphy is a dying art" and they weren't going to restock their nibs (he no longer works there, thank god, and there is a decent supply still, but not great).
Have a good trip!