Though I am not familiar with STEM hiring, I would think an important consideration at the Ph.D. level includes who specifically will you work with, what lab etc., how is the hiring support. My spouse is a humanities professor and his experience is, generally, while the specific program matters – which school – what matters even more in hiring is who did you work with.
Other than that, Wisconsin (where my son goes undergrad) is a great college town but winters are long and cold. To focus on the superficial, San Diego has mild weather year round. Also, cost of living is bound to be higher in San Diego, so compare how far your stipend will go in each city, not just how much it is.
Congrats on having great options for your Ph.D.!