Big non-profit organizations have highly paid leaders

— -- There is big money in running the USA's big non-profits.

CEO James Mongan of Partners HealthCare System, operator of non-profit hospitals in Boston, was the most highly compensated top executive in 2008 among those running the wealthiest foundations and charities that raise the most in donations.

Mongan, also a Harvard Medical School professor, was paid $3.4 million by Partners HealthCare, including nearly $1 million in deferred pay that was reported as a lump sum this year in accordance with IRS rules.

Museum of Modern Art director Glenn Lowry was No. 2 with 2008 compensation of $2.7 million, says The Chronicle of Philanthropy, which today releases its 17th annual pay rankings. Third was Steven Altschuler, CEO of Children's Hospital of Philadelphia, at $2.4 million.

"Partners HealthCare competes on a national stage for physician executives," and Mongan's pay "is in line with that of his national peers," says spokesman Rich Copp, who questioned the Chronicle's methodology. "We don't understand how Dr. Mongan could be No. 1 on this list when … data indicates that more than 15 non-profit hospital CEOs are more highly compensated."

Noelle Barton, manager of special projects for the Chronicle, says the ranking is of 325 of the largest and wealthiest charities and foundations and includes major private colleges, hospitals, museums and religious groups. About 1.3 million non-profits are required to report to the IRS, but the top 400 receive more than 25% of all private donations, and it's rare for a CEO of a smaller organization to be paid more than the leading non-profits' executives. However, Barton says some of the best paid may work for non-profits that receive the bulk of their funding from the government, and the Chronicle does not include those in its survey.

Donald Marron, chairman of the Museum of Modern Art compensation committee, says Lowry has "led MoMA through an intricate period of expansion and reinvention," that increased gallery space by 50%, attendance by 73% and membership fourfold.