Breaking Bad star Cranston landed the coveted Outstanding Actor in a Play prize for his turn as former U.S. President Lyndon B. Johnson in All the Way, which was also named Outstanding Play.
Harris, who wrapped sitcom How I Met Your Mother earlier this year (14), was honoured for his acclaimed performance as a transgender rocker in Hedwig and the Angry Inch, sharing the prize for Outstanding Actor in a Musical with Jefferson Mays, the star of A Gentleman's Guide to Love and Murder.
Other winners included Audra MCDonald, who was named Outstanding Actress in a Play for her portrayal of singing star Billie Holiday in Lady Day at Emerson's Bar and Grill, and Jessie Mueller, who was honoured for playing another music icon - Carole King.
Mueller landed the Outstanding Actress in a Musical award for the title role in Beloved: The Carole King Musical.
There were also two prizes for Sylvester Stallone's Rocky musical, which won trophies for Outstanding Set Design and Outstanding Lighting Design.
The awards, which honour the best of Broadway and off-Broadway talent, were handed out in New York City on Sunday (01Jun14).