As a Colorado resident, let me say that I'm pretty sure you'd be very happy in Boulder. According to USNEWS, CU-Boulder is #40 SoE. The other 4 criteria you have describe Boulder very accurately.
As for Fort Collins, I haven't been there much, but it is definitely geographically much more "out there" than Boulder. I think FC is about 60 miles north of Denver, while Boulder is about 25 miles northwest. The 25 miles between Denver and Boulder are pretty built up, at least by Colorado standards, while the drive to Fort Collins from Denver is pretty desolate.
Boulder is a bit more expensive than Fort Collins, but coming from the Bay Area, I'm not sure you'd notice much. It's all mighty cheap on the Front Range compared to anywhere near coastal CA cities.