Since other .js files are already there, that seems the right place. Then you'll need to find and update the references to them in your (X)HTML.
And you're right - for personal projects the gsap libraries are free. But you should sign up with them for their free licence. Free doesn't mean you may use it without permission.
https://gsap.com/pricing/
But if you ever do want to sell the epub you'll need to buy a licence.