Alien Covenant all the way.
But oddly, now that AC exists, I've grown to like Prometheus more. For years I considered Prometheus a "failed horror film" but now I've seen AC I've realised Prometheus isn't a horror film at all, it's just a straightforward science fiction one.
I feel the same way about 'PROMETHEUS'. Largely because it's become obvious the movie is a prelude of sorts, a prologue if you wish of a much larger, chaptered work in progress. I see 'ALIEN: Covenant' as Chapter 1. We need to see where the next movie is heading to really appreciate these movies. They should clearly be experienced as parts of a greater whole.
We are so accustomed to seeing these movies be fully self contained but these latest 'ALIEN' entries are obviously the first part of a much greater, Grander, experience. Scott said it was going to be epic. The next script has already been written. I think if it is (hopefully) eventually made, it will be better understood why these movies are structured the way they are.
Right now, as it stands, it's akin to an author releasing the prologue and first chapter of a book. We've had the introduction of the main themes of the prologue and the initial set up of the greater story has been set to unfold in chapter 1.
It would be a sad thing if it just ended here, just where the meat of any classic novel starts to emerge in Chapter 2. We really need to see what the next instalment is going to hold.
It is for this reason they cannot be easily separated and appreciated individually. It's an incomplete work; and that's obvious, too.