So just now I only googled 9 schools and all 9 have organ. From that I would conclude there are many many more. I would choose a school based on size, location, and “vibe” then look at their organ program. I could keep going and find others easily.
Organ and Church Music – Music (stolaf.edu) St. Olaf
Performance | College of Fine Arts (bu.edu) See organ section. BU has a grad program in sacred music too.
Program Overview: Organ | Oberlin College and Conservatory Oberlin
Organ | Lawrence University Lawrence
Program: Organ and Liturgical Music, M.M. - University of Hartford - Acalog ACMS™ Hartt
Organ | Peabody Institute (jhu.edu) Peabody
Thomas Handel teaches organ at New England Consrvatory
Ithaca Conservatory also has organ apparently but can’t find it on the site, saw an article about an organ student recital