Well it's really hard to compare, they're really very, very different games. Though if pushed to recommend one of them I'd easily side with the M.E series. Simply because it works well as a series, its a fun game with interesting characters and a fun, interesting storyline. Now Bioshock, is again a great game and I recommend it, I wouldn't recommend it over M.E but don't take me as someone selling the game short. It's a very good game, it's got great atmosphere and a stunning setting, there's a brilliant and creepy backstory to be found here and I can't do the game more justice. However as a series its kind of... Well... Not really a series. It doesn't feel like one. It didn't feel like a game that warranted a sequel and thus comes the failing of the sequel. Also I found the shooting in that game extremely clunky.
The sequel to Bioshock, some say its awful, some defend it... Me, I don't know I didn't far past the first few areas before I got bored and put something else on. However I was like that with most games when that came out. I just found the game unnecessary, with M.E, it's kind of left open for a sequel... Here... Not really. The ending kind of tied things up well. Though I imagine that if you play the second one first you won't have too much a problem with that. From what I played it still keeps some of the atmosphere and gameplay, warts and all.