"Most at nonprofits are not millionaires, and it's been tough times with many people not getting raises," she said. "But there's also a lot more focus on results, and that means paying for talent."

Hospital, Museum

The highest-paid executive in the Chronicle survey, which was obtained by Bloomberg Rankings, was Herbert Pardes, executive vice chairman of the New York Presbyterian Hospital board of trustees, who had 2010 compensation of $4.3 million, including a $1.71 million salary. Houston Museum of Fine Arts Director Peter Marzio, who died in December 2010, was second with $3.94 million, in part because of payouts triggered by his death, the Chronicle said. Pardes didn't return a phone call seeking comment.

Among traditional charitable groups, American Cancer Society CEO John Seffrin was fifth with a 2010 compensation of $2.08 million, including $1.49 million in deferred compensation and retirement. Boys & Girls Club CEO Roxanne Spillett, who retired last year after 34 years with the group, ranked eighth with 2011 compensation of $1.81 million, the Chronicle survey showed.

Cancer Society

Seffrin's compensation for 2011 was $764,135, including deferred compensation, and he declined an incentive for fiscal 2009 performance and agreed to a cut to his base salary of 6.4 percent, the American Cancer Society said in an e-mailed statement. In 2010, his total compensation was $2.4 million, which included $1.62 million in deferred benefits that will be paid at retirement, according to the statement.

Spillett's compensation included $1.18 million that was paid out as part of a previously reported retirement plan and the compensation was reviewed by PricewaterhouseCoopers LLC and her pay was "in line with industry standards and appropriate," spokeswoman Jan Still-Lindeman said in an e-mailed statement. The group doubled in size and tripled in financial scope during Spillett's 16 years as CEO, Still-Lindeman said.

New York University's John Sexton had compensation of $1.31 million, ahead of Yale University President Richard Levin's $1.19 million, according to the Chronicle data. Levin and Sexton didn't respond to e-mails seeking comment.

The top executives for the John F. Kennedy Center for the Performing Arts, Los Angeles Opera, Metropolitan Opera Association, Museum of Modern Art and the Art Institute of Chicago also made the list.

CEO Compensation

By comparison, the median total compensation for Standard & Poor's 500 CEOs rose about 6.2 percent to $9.6 million in 2011 from about $9 million in 2010, according to Equilar Inc., which gathers data on executive pay at public companies.