Cranston received a nod for his portrayal of President Lyndon Johnson in All the Way, which also nabbed a Best Play nomination, while McDonald was recognized for her lead performance in the play Lady Day at Emerson's Bar & Grill.
Harris, who has hosted the Tonys four times and won three Emmys for doing so, scored a nomination for playing the title character in Hedwig and the Angry Inch, a nominee for Best Revival of a Musical. (Watch videos of Harris here.)
A Gentleman's Guide to Love and Murder topped the field with 10 nominations, followed by Hedwig with eight.
The 68th Tony Awards, hosted by Hugh Jackman, will air Sunday, June 8 at 8/7c on CBS.