The Bujinkan Dojo is widely considered to be the last legitimate Ninpo school. The current headmaster or Soke, Masaaki Hatsumi, is carrying the lineage for these 9 ryuha:

Togakure ryu Ninpo Taijutsu

Gyokko ryu Kosshijutsu

Kuki Shinden Happo Bikenjutsu

Koto ryu Koppojutsu

Shinden Fudo ryu Dakentaijutsu

Tagaki Yoshin ryu Jutaijutsu

Gikan ryu Koppojutsu

Gyokushi ryu Ninpo

Kumogakure ryu Ninpo