The PDF is the original paper, as it appears on arXiv, so using PDF is natural.
In general academics prefer PDF to HTML. In part, this is just because our tooling produces PDFs, so this is easiest. But also, we tend to prefer that the formatting be semi-canonical, so that "the bottom of page 7" or "three lines after Theorem 1.2" are meaningful things to say and ask questions about.
That said, the arXiv is rolling out an experimental LaTeX-to-HTML converter for those who prefer HTML, for those who usually prefer PDF but may be just browsing on their phone at the time, or for those who have accessibility issues with PDFs. I just checked this out for one of my own papers; it is not perfect, but it is pretty good, especially given that I did absolutely nothing to ensure that our work would look good in this format:
https://arxiv.org/html/2404.00541v1
So it looks like we're converging towards having the best of both worlds.