Alien Covenant Script?

Unfortunately there is none released, about the closest you would get is Alan Dean Fosters  Novelization of Alien Covenant

As far as Prometheus... a quick Google Search and first place that pops up is via AVPGalaxy

http://www.avpgalaxy.net/files/scripts/script-alien-engineers-spaihts.pdf

http://www.avpgalaxy.net/files/scripts/script-paradise-lindelof.pdf

These provide a interesting read, and a Movie somewhat between those TWO would have made a better Alien Prequel and would have meant Alien Covenant would have not existed or at least would have not had to try and cover a lot of bases.