Well he's been portrayed as both, there really isn't a clear cut answer. At first he was a bad guy.. then he was a bad guy because he was brainwashed, then he was a good guy, then he was a bad guy. It really depends on the writer and what type of story they are trying to tell.

He is good guy because he had a lot of chances to kill snake eyes but he didn't

"He is good guy because he had a lot of chances to kill snake eyes but he didn't "

Like many other characters I don't think Storm Shadow can so easily be defined as hero or villain. So basically I think it's an impossible task to try and label him one way or another. 
 
The best characters (imo of course) are those who walk that fine line between good and bad.

The only time he was a villain (as defined by comic standards) was when he was brainwashed. He's actually a hero.

He's a hero, but I see him as neutral hero,

If you actually read all the original comics from there beginning Storm Shadow's first appearance is as a villain, but when you get his back story, he really isn't. He witnessed his uncle's murderer fleeing into a Cobra vehicle, and followed. He joined Cobra to find the assassin and kill him. However Cobra Commander knew Storm Shadow's intentions, but decided to use the vengeful ninja as a personal bodyguard, and made sure to keep Zartan far from him. During his time as a bodyguard, he was brainwashed. Even after breaking the brainwashing and joining G.I. Joe, Storm Shadow still felt jealous of his sword brother, and by code of the Arashikage, which states no ninja of the clan shall strike a fellow clan member, he decided to leave. He was again brainwashed by Cobra and forced to do the Commander's will. The only person Storm Shadow truly wished to kill is Zartan and Cobra Commander a close second. But due to all his jealousy, his vengeful spirit, and all the brainwashing he's suffered, his mind is truly unstable and neither Cobra or G.I. Joe will ever fully trust him. He is a threat to everyone making him one of those characters that can never be placed on a set side. He is and always will be a neutral character, even though he makes a better villain then hero.