For Cal Berkeley, drive up Berkeley hills, stop at Lawrence Hall of Science and drive along Grizzly Peak blvd. Sunset time is the best to view the whole San Francisco Bay with Golden Gate Bridge in the background.
For Stanford, drive along Skyline blvd 35 between Highway 92 and Page Mill Rd, you can stop by Windy Hill Summit and Silicon Valley vista point, and also Foothill Park's Vista Hill. All gives you some kind of panoramic view of South Bay and Silicon Valley, especially Stanford area.
If more time, drive to North Bay and drive up to Mount Tamalpais East Peak which will truly give you a full panoramic view of the whole bay area.
