And don't forget Yagyu Shingan Ryu, which is definitely taught alongside ninpo ryuha by none other than Tanemura Sensei of the Genbukan.
The thing about ninjutsu is that sometimes it appears to be an ad adendum to a formal bujutsu ryuha, and sometimes arises as a ryuha in its own right, and sometimes somewhere in between, as in Hattori Ryu.
Just to be sure, though, Yagyu Shingan Ryu and Yagyu Shinkage Ryu are quite different systems. From another of my posts here:
"Yagyu Shinkage Ryu Heiho is primarily a school of swordsmanship famous for supplying the Tokugawa Shoguns with teachers (Yagyu Munenori being probably the most famous). It was founded by Yagyu Munetoshi (Munenori's father, if memory serves), from the original source school of Shin Kage Ryu founded by Kamiizumi Ise-no Kami Nobutsuna in the mid-to-late 1500's (the official date of Yagyu Shinkage Ryu's founding is 1658 in most sources). Kamiizumi had based the Shinkage Ryu on the teachings of Kage Ryu, and had also trained in some other very famous systems, such as Kashima Ryu and Katori Shinto Ryu. He named his system Shin Kage Ryu (New Kage Ryu).
Yagyu trained in this Shin Kage Ryu and attained Menkyo Kaiden (full Mastership). He later (along with his son Munenori) introduced his art to Tokugawa Ieyasu, future ruler of Japan. Tokugawa was highly impressed, and employed the Yagyu family to be the official Swordsmanship Instructor for the Shogunate. He then founded his own system, which he called Yagyu Shinkage Ryu. Munetoshi's son Munenori has a number of famous stories about his skill, and his teaching methods, including meetings of mutual respect with the great Musashi Miyamoto. It is said that Yagyu Munenori helped Musashi in his research of two sword techniques, and the two of them also developed techniques to defeat two swords when only armed with one, known as Nito Yaburi. This is still taugth in one branch of the Yagyu Shinkage Ryu today.
In another branch, there exists a system of Iai (sword drawing), which is taught alongside the regular curriculum, known as Yagyu Seigo Ryu battojutsu, as well as another branch teaching Jo (4 foot staff) techniques by the name of Jubei no Jo, named after Yagyu Jubei, a popular character in Japanese books and film.
Yagyu Shingan Ryu, on the other hand, is a completely seperate Martial System. It was founded in the early 1600's by Araki Mataemon, according to the Goto-ha branch, also known as the Edo line, which refers to itself as Yagyu Shingan Ryu Taijutsu, although they also teach Kenjutsu, Bojutsu, Naginatajutsu, and Iaijutsu. It is said that Araki trained under Yagyu Munenori, and was such a gifted student that he was granted permission to use the name Yagyu in naming his own school by Yagyu Jubei.
The other popular line of Yagyu Shingan Ryu is refered to as Yagyu Shingan Ryu Heiho, and is based far more in armoured tactics. There are a number of unarmed sections, as well as weapon systems teaching Kenjutsu, Naginatajutsu, Bojutsu, Kamajutsu, Sojutsu, and others. This branch traces their origin back to Takenaga Hayato, who studied a number of systems, such as Toda Ryu (which exists in part today as Toda-ha Buko Ryu Naginatajutsu and Kiraku Ryu Jujutsu), Shindo Ryu, and Shingan Ryu. Shingan Ryu in particular was quite a hard system based in Sengoku period battlefield fighting, and was quite an influence on Hayato. Naming his own system Shingan Ryu (different characters), he travelled to Edo and met Yagyu Munenori, and was employed by the Sword Master. Again, the story tells that Hayato impressed Yagyu so much that he was given permission to use the name Yagyu in his own art, this time by Munenori."
Oh, and the Yagyu Shingan Ryu of Tanemura Sensei is just one aspect of the entire system. The unarmed alone is made up of 5 different sections: Suburi, Torite no Jutsu, Totte no Jutsu, Kogusoku Totte, Gyoi Dori, which can also be further divided into three groupings, Katchu Yawara, Kogusoku Yawara, and Suhada Yawara. Tanemura Sensei teaches the Katchu Yawara from the Suburi section, I believe, which he recieved from Sato Kinbei Sensei, not the entire system. Not that it isn't very worthwhile and interesting to learn, this is just to let you know.