In general, Pokemon with higher attack stats or more powerful moves are better than Pokemon with less weaknesses. Offensive Pokemon can win battles faster and spend less time dealing with stuff like confusion or evasion boosts. If you don't care about your time, you can just pick 6 random Pokemon, raise them to level 100, and win the game that way.
Another thing is that it's often not a good idea to overprepare for one Pokemon, like Cynthia's Garchomp. Yes, Cynthia is a difficult battle, but so are Wake, Candice, Cyrus, Lucian, and several other opponents. Preparing for one will hinder you against the others, and using a generally good team means generally doing well.
In Pearl, the water Pokemon with the best attack stats (and are also obtainable pretty early) are Empoleon and Gyarados. These are the movesets that I recommend. If you choose to go with Gyarados, you might want to catch a level 19 (or higher) Magikarp after getting the good rod, so it starts at a higher level and evolves faster.
Empoleon @ choice specs
EVs: 100 Spe
- surf
- flash cannon
- grass knot/hydro pump
- ice beam
Gyarados @ mystic water/splash plate/expert belt
EVs: 100 Atk
- waterfall
- dragon dance
- ice fang
- return/earthquake/stone edge