Cite Repository in manuscript: GitHub link "https://github.com/User/Code" VS zenodo link
GitHub can change in the future. You could push new stuff that changes the results you got and published. At the very least you should package a release and link that instead. I really hate methods sections that are just "this is my github repo no I've never heard of comments why do you ask". 

Zenodo doesn't change. That's the point. It's locked in.