Last year San Jose was Ranked as the #1 best performing city in the US by the Milken Institute. This primarily looks at growth of jobs, wages, and GDP (Gross Domestic Product, a good measure of what companies are actually producing and selling). For 2013, San Jose came in 4th place. Austin took #1, Provo was #2, and San Francisco was #3.
Just for fun I did a direct comparison on the stats between San Jose and San Francisco. 5-year and 1-year job growth was stronger in San Francisco, but 5-year and 1-year wages/salary growth was stronger in San Jose. High-tech GDP growth was slightly stronger in SF but San Jose took the cake in the entire study for total High-Tech GDP (it is double San Francisco's current Tech GDP).
Source: SVBJ, Best-Performing Cities