I like them both, a lot, and for different reasons.
HL2, of course, is much longer, highly cinematic, extremely well-paced, and has a gravity gun.
BioShock, on the other hand, really started sucking in the last third or so of the game. However, the overall story, the Randian philosophy of Rapture (well, at least it started out that way; the citizens of Rapture are actually pretty bad objectivists), and the mixture of steam punk inspired weapons and upgrades with powers made BioShock a real pleasure to play. In the first month and a half I had it, I played through it three times. I loved the atmosphere, too.
I'm abstaining from voting. I think both games are, overall, amazing.