His start in professional theatre came with the touring company of American Idiot. He was in ensemble and understudied the roles of Johnny and St. Jimmy, played by stars John Gallagher, Jr. and Billie Joe Armstrong, respectively, during the Broadway run. In 2013 and 2014, Boniello has appeared in many TV and film roles, including: Alien Dawn, Contest, Floored, Unrelated, and Happyish. He appeared in an episode of Jessica Jones in late 2015 as “punk kid.”

Boniello returned to theatre in 2015, when he performed in the Off-Broadway production of Brooklynite. He was also a member of the cast of Lin-Manuel Miranda’s musical 21 Chump Street and can be heard on the show’s original cast album. Later in the year, he was cast as the “Voice of Moritz” in the Deaf West Production of Spring Awakening, and stayed with the company with its transfer to Broadway. He completed his run at the Brooks Atkinson theatre on January 24, 2016. On April 13, 2018 it was announced that Boniello would be replacing Mike Faist as Connor Murphy in Dear Evan Hansen on Broadway. He made his debut in the role on May 15, 2018.

As a producer, Boniello is known for his work on the Broadway musical Hadestown, for which he won the Tony Award for Best Musical in 2019.