Extremely difficult choise between the two.
I´m a huge fan of James Cameron and he made 3 of 4, and Alien is one of the best works of Ridley Scott.
Even if both 1st movies are pure masterpieces, i have to go with the second installement of each.
Sure, T2 goes in the same vein as the 1st Terminator, making it look a bit on the update side, but, god damn, what an update
T2 is, IMO, one of the best comic book movies (without being based on a comic book, in the likes of the Matrix) ever made.
James Cameron is a huge comic book fan (said it in a couple of interviews), and it really shows in this movie.
Aliens is, simply, one of the best movies i´ve ever seen.
All in all, two of my favorite pair of movies, but i have to go with Alien, because of Aliens alone.