Honestly, I kinda feel like people automatically jump to 'ninja novel' and think it has to be some translated Japanese light novel series. There's a whole western tradition of it too, like 'Shogun' by Clavell has those incredibly tense sections with the ninja Mariko and the covert politics, but it's woven into a historical epic. Then you've got modern stuff like Barry Eisler's 'John Rain' series—the guy's a freelance assassin with a hyper-specific skillset for wetwork, but the tradecraft and the lonely, clandestine life is pure ninja ethos, just in a business suit. The secret clan element gets replaced by the shadowy world of intelligence contractors and yakuza connections. I think that's a more interesting angle sometimes, when the 'clan' is just the mercenary ecosystem you survive in.
For straight-up clans and missions, you can't go wrong with 'The Kouga Ninja Scrolls' by Futaro Yamada. It's the original source for that whole warring ninja clans trope, way before the anime. It's got that grimy, tactical feel where the supernatural elements are more like weird skills than magic. But I'll admit, the prose in translation can feel a bit dry compared to today's action-packed stuff. Still, it's the blueprint.