Question

What water-type Pokémon(s) (Legendary/Non-legendary) has the highest base Special Attack stat?

Answer 1

(This list is from the first Water-Type on the list to the first Non-Legendary Water-Type)

Primal Kyogre: SpA = 180

Kyogre: SpA = 150

Palkia: SpA = 150

Mega Blastoise: SpA = 135

Source: [Serebii][1]

Edit: Without Megas or Legendaries, the highest base SpA stat would be Clawitzer at 120. (Credit: MeloettaMelody)
[1]: http://www.serebii.net/pokedex-xy/stat/sp-attack.shtml

Comments

You might want to add that if you ignore both legendaries and megas, then it is Clawitzer with 120 base Special Attack.