I like almost every Water type Pokémon around but I didn't want to choose more than three. It seems that my Gen. 3 bias is strong this week:
Wailord is not only my favorite Water type Pokémon but it's also my favorite Pokémon of every type. Whales are really unique creatures that have always been my favorite animals, which is what makes Wailord my favorite. It also cool to watch people ride them in the anime because they look so small xD.
Who doesn't like Ludicolo? These fun little Pokémon are always jammin' and providing good times. You can't beat the sombrero/duck beak combo. They also remind me of when I used to play Colosseum and the Miror B battles.
My third choice is Crawdaunt line. I just used one in my last Emerald playthrough and I really liked it. I've also been watching the AG series of the anime and Ash's Corphish is quite the character.