Tough choice, both represent excellent early works from Ridley Scott and James Cameron, and both pushed the boundaries of the Sci-Fi Horror & Sci-Fi Action genres. Alien is more unique and broke new ground with a lead female protagonist with a deep focus on tension,mystery, horror and the feeling of isolation and the unknown.
Aliens on the other hand, dialled the action upto 11 and focused on character relationships/ world-building and the effects that the Alien creature had on the colonists. We begin to understand more about the creatures breeding habits and the fact that a Queen exists as if they are like a hivemind. I would give the edge to Aliens, but only by a smidge.