The ceremony was held in the East Room at the White House. The Medal of Freedom is the country's highest civilian award.
One medal was given posthumously to John "Buck" O'Neil, a player and manager in the Negro League and Major League Baseball's first black coach.
King was honored for his half century as "King of the Blues" and Lederberg for achievements that include pioneering work in bacterial genetics and working with NASA to look for life on Mars.
Other recipients included Ruth Johnson Colvin, founder of Literacy Volunteer for America; Norman Francis, president of Xavier University, a historically black Catholic institution in New Orleans; historian Paul Johnson, a British citizen; historian David McCullough; former Transportation Secretary Norman Mineta; former New York Times columnist William Safire, a former speechwriter for President Richard Nixon; and Soviet dissident Natan Sharansky.