they're both very safe surgeries these days, so I wouldn't really worry about that piece of it.
what most people will tell you is that if you have issues with GERD, bypass is usually the way to go. Otherwise, it pretty much comes down to personal preference. There may be other health issues that would make one surgery more appropriate than the other, but that's the major one. Your surgeon will be able to explain the differences and recommend one or the other depending on your particular health issues (if you have any), although in the end, it's ultimately your choice.
I had the bypass and have been very happy with it.