A place to host static HTML+JavaScript that can be referenced from a paper?
GitHub Pages web hosting really is perfect for your needs, but you might also want to consider FigShare. You'll get a DOI, which makes it easy for people to cite your HTML application. You could zip up your application using only local references so your app will be downloadable and usable as long as HTML 4/5 browsers exist. Until March 2015, content on FigShare was shared through an international alliance of libraries (CLOCKSS), but alas no longer.