In my opinion, it's all in the fingers. Perfecting the way you touch the string, and how you play it, can cut out a lot of noise. Or at least, that's the conclusion I came to.

But I think maybe you are just using too much gain/distortion. Which is a mistake a lot of guitarists make. When using little distortion, you will automatically have less noise. Yet, it will be harder to play, cause the distortion won't cover up any mistakes.

I hope this helps, if not, ignore this post. ;)