Apple’s Tim Cook is Bay Area’s most highly paid CEO

It’s good to be Tim Cook.

With 2011 compensation of $378 million, the Apple chief executive ousted Oracle’s Larry Ellison as the Bay Area’s most highly paid CEO of a publicly traded company, according to a survey by the San Jose Mercury News.

In comparison, Ellison’s pay package was $77.6 million, including $62.6 million in option awards, up 10.6% from a year earlier.

The top 10 included just one woman, Hewlett-Packard’s Meg Whitman, who, despite taking a $1 annual salary, made $16.5 million last year.

Other notable tech figures include Intel’s Paul S. Otellini ($17.2 million, No. 9 on the list), EBay’s John J. Donahoe ($16.5 million, No. 11), AMD’s Rory P. Read ($15.6 million, No. 13) and Cisco’s John T. Chambers ($12.9 million, No. 16).

The Mercury News, citing its annual What the Boss Makes survey, said median pay for Bay Area chief executives was $3 million. The paper reviewed CEO salaries, bonuses, stock grants and options reported by the Bay Area’s 198 biggest publicly traded companies.

Of the chief executives who had been with their companies for at least two years, 100 saw their pay increase in 2011, 62 saw it decrease and five had their pay remain steady. The median increase was 33%.

The paper noted that executives might not profit from stock and options granted during the fiscal year until they are vested or exercised in the future. In Cook’s case, that meant his actual take-home amount was $1.8 million in pay and a bonus.

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