Like other people have mentioned when Senpai visited Nagatoro's house he saw a shelf of her trophies and a picture of her in a martial arts gi smiling with a medal. Her older sister teased Senpai about it briefly.
With how often Nagatoro kicks Senpai I thought the martial art might've been taekwondo, but it's pretty unlikely since it's a japanese manga.
Her stance this chapter - with the hopping - reminds me most of sport karate (i.e. point based instead of full contact - thanks Batuque lol).
Senpai did say it wasn't karate but in-story what would he know? He would probably be thinking of traditional karate - horse stance, cat stance, reverse punch, etc.