First off, enjoy your trip to my fair city. Also, bring warm clothes. Yes, it will be May. And California. That doesn't matter, it will get cold and damp anyways.
There's a huge PEARL at 6th and Market.
The Mission District has http://www.needles-pens.com/
on 16th Street. For yarn and stuff like that there is www.imagiknit.com
is awesome. It's like a gym...but for crafts. If the name didn't tip you off.
Lower Haight has a ton of craft stores.
This is non-craft related but also go to http://www.826valencia.org/store/
in the Mission. It is also known as "the Pirate Store" (for piracy supplies) and next to it go to Paxton Gate.
I'll think of more.