The NFL tells SportsBusiness Daily that commissioner Roger Goodell was paid $44.2 million for the 12 months ending March 31, 2013. For an inappropriate yet telling comparison, that is more than any football player has ever been paid—and almost exactly twice as much as the current highest AAV contract will pay Aaron Rodgers next season.
The breakdown shows a $3.5M salary and a bonus of more than $40M. ($9.1 million of that was deferred from the previous year.) Goodell's bonus is tied to unknown benchmarks, though we know some involve league revenue, and, many believe, rewards for the pro-management CBA that ended a 2011 lockout.
Goodell's salary has increased astronomically since taking over—for the fiscal year ending March 31, 2012, his take-home was $29.5 million. The year before, "just" $11.6 million.
Goodell is by far the highest-earning commissioner in major pro sports. MLB and NBA aren't required to report salaries, as the non-profit NFL must, but Bud Selig and David Stern are believed to make between $20 and $30 million. (New commish Adam Silver's pay is presumably much lower.) For the most recent year available, Gary Bettman earned $8.3 million.