d20 Modern, probably with Blood & Fists [volume 2 has a Ninja advanced class].
"Ninja" is a fairly broad concept, so I think you could come up with a good range of characters.
With just d20 Modern, I'd probably start everyone with a few levels of Infiltrator and a few levels of Martial Artist [to represent your basic ninja stealth & combat prowess]. But they could come from a variety of basic classes and have levels in other advanced classes --- maybe one is the planner /guerilla warfare expert [Smart Hero / Field Officer], another is the master swordsman or archer [Archaic Weapons Master], another has mastered the mystical aspects of ninjitsu [Dedicated Hero].
And if you want to go that route...a few levels in Occultist or another magic-using class would work.
Or maybe one guy is a half-Japanese Army officer, a decorated Ranger trained in some more mainstream martial arts like jujitsu, who is brought in to lead the team in the hopes that he can bridge the gap between ancient Japanese traditions and modern military discipline.
With Blood and Fists, there's a great deal of room to customize different schools and subschools of ninjitsu --- maybe these guys represent a number of different ninja clans.