Having grown up out west, I was surprised to discover how comparatively few American wines were available in Boston. I'd imagine a lot of it stems from the fact that shipping wine from the west coast isn't that much less expensive than importing wine from Europe.
While I can't think of anywhere around town that has a majority of [potable] California wines by the glass, a few places you might try:
Les Zygomates - the vast majority of their wines are from France and Italy, but their online menu currently lists 10 American wines by the glass.
Troquet - you won't exactly be deluged with a flood of CA wines here either, but the wine program is good enough that it if it's on the menu, it will likely be great.
T.W. Food - three of their four currently featured wineries are from California. I sampled a few of these wines with a tasting menu last week and enjoyed them very much.
Places about which I know nothing that might merit a visit: CaliTerra, Vintage Lounge, Vinalia, all in the financial district.