That's definitely the short list of "affordable" public golf near San Jose. I haven't played the redesigned San Juan Oaks, so can't comment on it. Coyote Creek and Cinnabar are literally 10 minutes from the location where the MidAm qualifier is being held ... we actually bicycle past Coyote on the nearby bike trail. Coyote has the benefit of having two courses, so with mid-summer daylight, it's easy to get 36 in.
Affordability-wise, Harding is getting up near Pasatiempo for non-residents, and the Ocean Course at HMB is relatively pricey as well. Not sure the Old Course at HMB is worth the drive ... a lovely Palmer design that winds through a housing development, but except for the 18th (which is magnificent), there's nothing really special or memorable.