I think it is dragonite but I think they're adding mewtwo soon; will he be stronger?
Yes, Mewtwo is the strongest pokemon.
But I thought he wasn't in the game...?
Mewtwo will be the most powerful when he's introduced into the game - his max CP will be 4144.75 according to this website: http://uk.ign.com/wikis/pokemon-go/Pokemon_Max_CP
But until then it's definitely Dragonite!