When taking into account various factors such as base stats, movelist and abilities, Salamence would win by a small margin. This is chiefly due to the difference between the two Pokémon's base attack and speed.
Salamence has a base attack of 134, which is just one higher than Dragonite's at 133. Also, Salamence's base speed is noticeably higher, at 100 versus Dragonite, which is only 80. This meana that Salamence would get an extra turn every five turns and therefore, could do more damage. Other factors to consider are Salamence's increased base hitpoints and special attack, which are both important stats in dragon Pokémon.