From 1988 to 2003, Cynthia was in a relationship with schoolteacher Danny Mozes. They have two children together. In June 2018, she revealed that her older child is transgender. In 2004, she began dating education activist Christine Marinoni.
Cynthia and Marinoni became engaged in April 2009, and married in New York City on May 27, 2012, with her wearing a custom-made, pale green dress by Carolina Herrera. Marinoni gave birth to a son in 2011. Cynthia identified herself as bisexual in 2012 but now identifies as queer.
