He holds an empty hand in the air. It's a human greeting, but Pokémon understand human speech so maybe they understand body language too?

Like you would if you wanted to approach any skittish countryside critter, he makes eye contact with the Gyarados long enough to make sure he's seen, and then drops his gaze as he slowly walks forward.

If the Gyarados starts looking too agitated, he stops moving for a bit.