Harris, 40, who has hosted the Tonys four times, earned his first nomination for best actor in a musical for his role in Hedwig and the Angry Inch. He was joined in that category by Ramin Karimloo (Les Misérables), Andy Karl (Rocky) and Jefferson Mays and Bryce Pinkham (both for A Gentleman's Guide to Love & Murder).
Cranston, 58, and O'Dowd, 34, both earned their first Tony nods and will square off in the category of best actor in a play – for All the Way and Of Mice and Men, respectively. Also in the category: Samuel Barnett (Twelfth Night), Mark Rylance (Richard III) and Tony Shalhoub (Act One).
Two musicals earned the most nominations overall: A Gentleman's Guide to Love & Murder, with 10, and Hedwig, with eight.
The nominations for best actress in a play went to Tyne Daly (Mothers and Sons), LaTanya Richardson Jackson (A Raisin in the Sun), Cherry Jones (The Glass Menagerie), Audra McDonald (Lady Day at Emerson's Bar & Grill) and Estelle Parsons (The Velocity of Autumn).
Best actress in a musical nominees are Mary Bridget Davies (A Night with Janis Joplin), Sutton Foster (Violet), Idina Menzel (If/Then), Jessie Mueller (Beautiful: The Carole King Musical) and Kelli O'Hara (The Bridges of Madison County).
Washington had been considered a front-runner for a nomination for A Raisin in the Sun but was left off the list. Radcliffe (The Cripple of Inishmaan) and Williams (Cabaret) were also snubbed.
Other high-profile actors who failed to earn nominations included Daniel Craig and Rachel Weitz (Betrayal), Ian McKellen and Patrick Stewart (the double bill of No Man's Land and Waiting for Godot), Zachary Quinto (The Glass Menagerie), James Franco (Of Mice and Men) and Michael C. Hall (The Realistic Joneses).
The nominees for best play are Act One, All the Way, Casa Valentina, Mothers and Sons and Outside Mullingar.
Nominated for best musical: After Midnight, Aladdin, Beautiful: The Carole King Musical and A Gentleman's Guide to Love and Murder.
See all the nominees at the Tony Awards website.
The nominations were announced from New York's Paramount Hotel by Jonathan Groff of HBO's Looking and Lucy Liu of CBS's Elementary.
The 2014 Tony Awards, hosted by Hugh Jackman, will be broadcast from Radio City Music Hall in New York on June 8 at 8 p.m. ET/PT on CBS.