I'd go Summoner, use traits to grab the stealth skills they supposedly have, maybe create a new feature, based on the Skeleton Summoner feat to allow summoning zombies, with the Juju Zombie acting as Human Puppets, using the Expanded Summon Monster feat to choose class levels for the Juju zombies or skeletal champions. As a GM, I would allow you to hold off on choosing your new monsters until you find a corpse, allowing you, between adventures or with downtime, to turn the corpse into your puppet.
Oh, I'm a fan of spheres of power for this. You can take any number of things from the conjuration sphere to customize however many puppets you want, change them up relatively easily to let you rebuild puppets every few sessions to be tinkering with your designs if you'd like, and take other spheres for your personal ninja abilities. If you take no martial abilities at all a pure caster can invest easily 40+ different abilities into 1-5 puppets (table law may apply, I'd say limit to 2 puppets on the table consistently, 3 when absolutely needed, and maybe let another player control one or two so your turns aren't so long).