Should jQuery DOM Ready code be in the page with the HTML or separate JavaScript file?
I don't know if it is good practice, but in my eyes it would be cleaner, since you have several JS-files at this point, to separate markup, layout and JS completely. So $() would reside in a .js-File.

In some cases, when you only have a few lines of JS or -on the other hand- if you have to care for every millisecond to deliver a good page experience, it would make sense to embed JS in the html-file and retrieve the non-critical JS at later time dynamically.

It depends on your usecase.