Elliott “Lee” Sander, chief executive of the Metropolitan Transportation Authority, is stepping down, but the agency says it’s not because of the controversy over the payroll tax Albany just approved on employers in the New York City area.

That tax — 34 cents per $100 of payroll — will be levied on businesses, hospitals, governments and non-profit agencies in the 12-county area served by the MTA, including us here in Westchester, Rockland and Putnam.

The MTA says Sander’s exit has been in the works for a while. Here’s the entire statement issued by the agency:

Governor Paterson today accepted the resignation of MTA Executive Director and Chief Executive Officer Elliot G. Sander. Mr. Sander offered his resignation to the Governor earlier this year in anticipation of yesterday’s passage of legislation that joins the Chairman and CEO positions at the MTA. Mr. Sander’s resignation is effective May 22, 2009, ending a tenure that began January 1, 2007.

MTA Executive Director and CEO Elliot G. Sander said: “It has been a great honor to lead the 70,000 hard-working men and women who run the world’s greatest public transportation system. I am tremendously proud of our accomplishments making the MTA a leaner, more efficient and effective organization. Each of the MTA’s agencies is performing at peak levels, the relationship with our employees is dramatically improved and we communicate more frequently with our customers. The integration of the MTA’s three bus companies, the merging of back office functions across 7 agencies and the introduction of line general managers on the subway system will save the MTA millions and improve the agency’s performance. New innovations like rider report cards, text message alerts and Select Bus Service have improved the customer experience. There is more work to be done, but I leave confident knowing the MTA is headed in the right direction. I am grateful to Governor Paterson and Governor Spitzer for this wonderful opportunity. I wish Governor Paterson the best of luck in choosing a successor who will build on the progress the MTA has made over the past two and a half years.”