After playing Ninja Gaiden (the original one) again, I have to say that the bosses in this game (except the first two) have high factors of pissingmeoffedness.
However, the one enemy I cannot stand is the eagle.
It takes 3 bars of life on contact (as opposed to a pretty small 1 bar taken by a ROCKET LAUNCHER).
It moves fast.
It has the second smallest surface of the game (the smallest being the slightly less annoying bats)
And since the game is buggy, they can spawn sporadicly for no reason after you killed them. (Apparently, they are generated as you step on a specific tile column and if you do not move from the trigger, the game assumes that since you killed the eagle, it never was generated.)
So yeah, if you are afraid of ninjas, invest in eagles. They will defend your base better than twin hopping statues that spit out brain looking balls of gas.
(In fact, I am convinced that 15 eagles would be harder to beat than the last boss of the game.)