While you can always use 本部【ほんぶ】 for headquarters, a stylish way to say 本部 (of a martial art or a religion) is 総本山【そうほんざん】.
This refers to a name of a place (town), a name of a building (temple, shrine, etc), or a name of a group (institute), depending on the context.
天台宗の総本山は延暦寺です。 Sohonzan of Tendai-shu is Enryaku-ji temple.
柔道の総本山は講道館です。 （BTW, 講道館 is the name of a institute as well as the name of a building）
Edit: It was pointed out that 総本山 is too grandiose for rather small and non-Buddhist groups like Geido-Kenpo-Ninpo-Ryu. Although 総本山 is a grandiose word and has roots in Buddhism, I think it can safely be used metaphorically for non-Buddhist groups, especially those related to Asian traditions. (Perlの総本山は perl.org です, etc.) Removing "総" and just saying "本山" sounds less grandiose (General HQ vs. HQ, I think). But if your group is a really small one, don't use (総)本山 (or maybe 本部, either)