Andrew Beinert scored 18 points for Holy Cross (13-12, 8-2 Patriot League) as the team fell out of a 1st place tie in the league with the loss.
Beinert sparked an 11-0 run to help Holy Cross take a 32-30 lead at halftime.
Boon converted three consecutive 3-pointers in the second half, sparking a decisive second half rally that helped Bucknell (6-19, 3-8) take a 44-32 lead with 16:23 left in the game.
Holy Cross cut the lead to 44-39 on a 3-point play by Colin Cunninham, who finished with 13 points.
Darryl Shazier helped keep the Bison in front, scoring 17 points -- including 5 of 7 3-point attempts.