I would choose both, actually, because Gyarados is a reliable tank and sweeper at the same time, and Quagsire is great for a Water-Ground in the beginning, for the Fire gym. However, I, through personal experience, wouldn't keep Wooper/Quagsire as a permanent team member.
I would keep the Quagsire boxed and sometimes use it for Fire specialists. Both are great Pokémon on a team, but only when you need them. If you were to keep the chosen one permanent, definitely go with Gyarados