With each and every Pokémon there seems to be something about them that is based off of one thing or another. For some Pokémon this can be pretty obvious, but others not so much. In the case of Greninja it is obvious to see what it is based off of, but I'm gonna go ahead and explain it anyway.
When looking at Greninja it is obvious to see it is based off of a frog, quite possibly one of the horned species due to the spiked protrusions above its eyes. Also, the shape and color of it is similar to a splendid leaf frog, and the bubble-like protrusions on its body may be based on toad parotoid glands, possibly referencing the traditional myth of toads causing warts. They could also just be remnants of Froakie and Frogadier's foam though. As the name implies it is also based off of a ninja. While not entirely obvious, the way Greninja wears its tongue around its neck––regardless of how weird it is––and its overall posture in battle does give it that ninja feeling.
As for the name, Greninja, it is pretty straightforward. The name is a combination of the words grenouille (French for frog) and ninja. As for its Japanese name, Gekkouga, it is a combination of the words geko (croak) and Kōga-ryū, an ancient school of ninjutsu. Sounds pretty cool if you ask me.