Mudkip's best moveset in Pokémon GO is Water Gun and Stomp, with 7.92 damage per second, and it can deal 90.2 damage before Mudkip faints. This is true when battling in neutral weather.
All Mudkip movesets ranked
Here is a complete list of Mudkip movesets in Pokémon GO, ranked by their DPS and TDO. You can change the weather and the opposing Pokémon.