How I Met Your Mother actor Neil has hosted the awards four times but this is his first nomination for his lead role in the revival of Hedwig and the Angry Inch, which gained seven other nominations including Best Revival of a Play.
Neil Patrick Harris, Idina Menzel and Chris O'Dowd lead Tonys nominations
Idina won her first Tony ten years ago for her role in the hit musical Wicked, and made her return to Broadway this year in the nominated musical If/Then.
The show has also been nominated for Best Score.
Irish actor Chris O'Dowd gained a nomination for his performance in Of Mice and Men, which also stars James Franco, while British actor Mark Rylance was nominated twice, once for Best Leading Actor in a Play for his performance in Richard III, and Best Featured Actor in a Play for Twelfth Night.
Going up against Mark is fellow British actor Stephen Fry who is also nominated for his work on Twelfth Night.
A Gentleman’s Guide to Love & Murder garnered the most nominations with nine, followed by Hedwig and the Angry Inch and After Midnight.
It’s been a busy year for Idina who also voiced the role of Elsa in Disney's smash hit animation Frozen.
Idina Menzel sings at the Oscars 2014
The film won two Oscars and Idina sang at the 2014 ceremony although her performance was overshadowed by John Travolta's flub of her name.
John set off a firestorm of criticism when he said, "Please welcome the wickedly talented, one and only Adele Dazeem," as Idina came on stage to perform Let It Go, winner of Best Original Song.
Idina has also recently revealed that Anna Wintour is helping her choose her Met Ball dress.
"I am excited to be attending," she said, adding, "I don't think I can tell you about my dress because Anna Wintour is helping me so I don't want to say the wrong thing!"