It's much better to delete old code than just commenting it out.  By commenting it out, there becomes a lot of wasted space in the files, and it's not necessarily that instructive.  Why is it there?  Why is it commented out?  Is it wrong?  

A better practice is to just delete it, and make it clear in your commit message what you're doing.  That's the great thing about git, you can always roll back changes, and with GitHub, it's easy to see what was changed.