Ah you're missing out by not including GTA III among the list. You can't not include it. Anyway I suppose if you want to choose between these two. I think San Andreas wins it for me, mainly because of how much stuff you could do.
Vice City though, had the better story. It's hard to pick which one had the best soundtrack though.
GTA III deserves some rep though. It's what brought GTA into the 3D world and it's what made me a fan of the series to begin with. GTA III's protagonist isn't great though, he never speaks, which always bugged me. That's why I was so glad Vice City gave us a protagonist that actually speaks. But yeah, GTA III is still a great game.