The Team With the Highest Median Salary in MLB 2006: Boston Red Sox - $ 3,023,894 2005: New York Yankees - $ 5,833,334 2004: New York Yankees - $ 3,100,000 2003: New York Yankees - $ 4,575,000 2002: Seattle Mariners - $ 3,333,333 According to USA Today, the highest level median salaries have gone down since 2002...FWIW. By comparison: 2006: Milwaukee Brewers - $775,000 2005: Milwaukee Brewers - $420,000 2004: Milwaukee Brewers - $400,000 2003: Milwaukee Brewers - $428,000 2002: Milwaukee Brewers - $1,100,000 link