Heroes of the East and Ninja in the Dragon's Den - two Hong Kong classics that feature ninjas prominently.
Then of course there's Revenge of the Ninja and Prey for Death. I like Ninja Assassin, too, but I felt it was just too slick in certain areas. The CGI just kills certain scenes for me. I thought the first Teenage Mutant Ninja Turtles produced by Golden Harvest was great, too. Way better fight choreography than I would've ever expected from a bunch of guys in rubber suits.
I also liked the depictions of ninjas in the second season of Daredevil before the whole K'un L'un reveal.