Both legendary excellent movies in their own right, but I´d have to go for Alien.
Mainly because I like that type of movie, it was very original at the time, and you hardly see the alien. The suspense is built up as the story line goes on. And the artistic influence/input from H.R Giger is masterfull.
Really hard to compare these two movies. Blade Runner is certainly more cerebral of a movie and unfolds a lot like a novel but Alien is the better movie for me. Blade Runner is definitely a great movie but it's one of those movies that i really don't need to ever revisit. That is probably a testament to the filmmaking because even though it's been probably a decade since i've last seen Blade Runner i can still remember it as though i just saw it. Alien is a movie that i can watch time and time again.