The New York City comptroller’s office revealed today that the Yankees underpaid their rent by $11 million between 2003 and 2006, including taking the same “stadium planning” credits in 2006 that they took in 2005. The good news: They’re paying it back. Slowly.

City comptroller (and still possible 2009 mayoral candidate) William Thompson issued his long-awaited audit today of items the Yankees deducted from their city rent for “stadium planning” costs, as allowed under the lease they got from Rudy Giuliani as a going-away present in 2001. How long-awaited? The audit (PDF here) covers January 2003 through December 2006, which is so far back that Raul Mondesi and Sterling Hitchcock were still in pinstripes.

The comptroller’s conclusion, as Juan Gonzalez first reported in this morning’s News: The Yanks improperly underpaid the city by more than $11 million over that four-year span…