Surf is better in most cases. It does more damage than Water Pulse, and while Water Pulse has the chance to confuse an opponent, you'd be better off with brute force in this case. The only times Water Pulse is better is if you can't get Surf (i.e. partway through a playthrough) or in double battles, where Surf hits your own Pokemon as well. But in that case, why not use Scald or Hydro Pump over Water Pulse?
Always use Surf, unless you can't get it yet, or it's a double battle (in which case use Hydro Pump or Scald). Water Pulse should almost never be considered.
Hope I helped!