Story in GTA 4 was the best imo.
If you listen to the dialog it gets pretty depressing. To me Grand Theft Auto 4 has the best story line, while GTA:SA has the best gameplay for obvious reasons. Its good to know though with Red Dead and LA: Noire i see Rockstar aiming for an awesome story which i value the most out of a game for some strange reason.
To me though Niko Bellic will always be my favorite character from the Rockstar series.
It's between IV and San Andreas for me. I really liked the depth San Andreas had in terms of things to do, but GTA IV really raised the bar for the franchise with it's story and characters. I still think Niko is one of the best protagonists in any video game.
GTA 1 was the best, but from the list I went with Vice City. It was the first of the 3D games I got into (skipped 3 for some reason) and it had amazing music. San Andreas had nice detail but something about it just felt a bit dull.. Dont think I liked the 90's hood setting very much. Although I confess I was absolutely inlove with the bikes and doing bike stunts! 4 was awesome too, just not as nostalgic and no good music (yes music makes a big difference in a GTA game since you spend almost all your time in the car).