Rif: I do not have personal experience (meaning my own children) but I have seen bochurim from my neighborhood (who I would say were in the same category as you describe your son) who blossomed in (alphabetic order):
Yeshiva Adereth Hatorah (Rabbi Senter)
Yeshiva Ateres Yerushalayim (AKA “AJ” )
Yeshiva Mercaz Hatorah
Yeshiva Toras Chaim
Hatzlacha!