You can trust my opinion as I have used both throughout my game: Kingdra in Gen V and Greninja in Gen VI. Greninja is great as a special or physical sweeper as it's movepool is satisfyingly big, and is used with a life-orb or a choice scarf. A Kingra with swift swim is clearly going to be found on a rain team, so a modest, choice specs one using surf is going to do BEAST damage in the rain, and in that situation probably better than Greninja. However, Greninja is a much better lead.
Weaknesses: Kingdra has 2: dragon and fairy; Greninja has 5 (until a move is used obviously): grass, electric, bug, fighting and fairy.
Hope this helped and stuffz!