Bay Area: Linda Vista Native Plants (Saratoga)
Larry has a wider selection than most Native Nurseries I've been to. He seems keenly interested in manzanitas, ceanothus, dudleya, and bulbing plants like calochortus. His stock is a mixture of Bay Area, Central Coast, Channel Island, and San Diego species with a smaller selection of Sierra Nevada, North Coast, and SoCal species. The nursery is pickup-only by appointment. My impression is that Larry would rather lose a sale than sell an unhealthy plant, so be prepared that part of your order might not be there if he doesnt like the look of it. I highly reccomend this nursery if you are in the Bay Area
California Flora Nursery (Just outside Santa Rosa)
One of the great institutional nurseries of California native gardening. Their overall stock is unmatched, but only a small fraction is available for purchase at any given time. This is the only nursery that commonly carries clones of the Vine Hill Manzanita other than the common hybrid cultivars (such as Howard McMinn, Sentinel, Harmony). The non-hybrid species is usually (but not always) low-growing, with smaller darker leaves and more delicate flowers, absolutely stunning IMO. The pure species selections will be named stuff like "VHP - A11 'low growing'" or "VHP - B3 'tall one'" since they are from stock also used for ex-situ conservation plantings
This nursery is also responsible for the introduction of many popular cultivars, especially Ceanothus. Some of my favorites are Ceanothus "Better than Ray Hartman" and Arctostaphylos "Reina de la arena". Their selection is wide, but especially covers the North Bay Area, Northern Coast, and Inner Coast Ranges. Good variety of oaks, pines, cypresses, grasses, and even annuals. In my opinion, it's worth the trip from anywhere in California.
"quotes" are my words, i will write up a few more when i have time. Those are my favorites however