Gyarados and Pelipper have the same type, so I definitely wouldn't recommend using both at the same time. However, they're different enough that I don't know for sure which is better. Pelipper is better earlier in the game and relies more on special attacks like surf and ice beam (and wing attack before it evolves). Gyarados is useless early on and later becomes good at using physical attacks like thrash, return, and earthquake.
I will say that Gyarados is worse than both Swampert and Zangoose, so use Gyarados only if you don't want to use Swampert or Zangoose for whatever reason.