Hunter scored 18 of his points in the first half alone, when the Lions built a 35-18 halftime lead. He was named tournament MVP.
Devan Veeder added 11 points while Tony Franklin had 12 rebounds for Lyons.
Andrew Short led York with 11 points.
It was the 16th sectional title in school history for Lyons, but their first since 2006.
Lyons will next play Wednesday in the state qualifier against the winner of Clyde-Savannah and Mynderse, who won the C3 and C1 titles, respectively.