Where in MODx can I put Javascript code?

You actually can see best practice here: https://github.com/smooth-graphics/modx-boilerplate/tree/master/assets/templates/main in header and footer. It’s not easy and you have to understand how the DOM-load is working in a browser to know where to put into.

Best practice is to do it before closing body tag

Not if you’re loading it asynchronously - the current version of Google Analytics tracking script, for example, goes in the head and loads asynchronously.