Please do not listen to the man who knows nothing about ninjutsu telling you it's for spies.
Kenpo is usually used in reference to arts imported to Okinawa and Japan from China (as in Shorinji Kenpo), and are, while uniquely Okinawan or Japanese, influenced originally from China. USSD Kenpo centers tend to claim this sort of lineage, though Ed Parker, though my experience with them was lackluster.
Ninjutsu is usually used as a substitute term for the teachings of the Bujinkan, Genbukan, or Jinenkan. Typically, what's being referred to is the taijutsu (body skills) of the art. You might get a better idea or some good answers to your questions about the Bujinkan by following the link to my website below.
Ultimately, which you do should be dependent upon your impressions of the instruction you'd be receiving -- a great instructor in one is better than a lousy instructor in the other. Go to each, inspect the classes, see what they offer, and make your decision on your gut instinct. Be critical and enjoy! You'll do well, whichever you choose.