Can't really stand either film, but my vote has to go to Prometheus because at least that movie made a commitment to what it wanted to be, which wasn't an 'Alien film' per se. It was just kind of a dangerous space adventure, not really a monster movie. Covenant can't really make up it's mind. For the first half it's like a darker, less convoluted Prometheus. For the second half, it's like a shitty, unremarkable version of Resurrection: "let's see how we can eject the xeno from the ship before we run out of time or people" type narrative. The only thing new about it was a shower scene...which has been a cliche of horror films since Psycho in 1960.
Also, in Prometheus, there's at least some characterization, even if much of it makes no sense (scientists afraid of scientific discovery, etc.). I've seen Covenant twice and basically don't know the majority of the characters' names or what distinguishes them. I remember that one woman is Jewish (I think), but I have no idea who her 'partner' was, which is important because that's a central conceit of the plot. I'm assuming she lost her partner, but it never seemed like she cared. I remember that two guys were gay, and that it isn't clear that's the case until one of them dies. No idea what their names were or what made them individuals with personalities. One of them was the security chief, so I knew his job but that's it. Obviously I remember Danny McBride because he's a star, and the main character because we spend more time with her. Prometheus made some effort to convince me I should care about at least some of the people in it; Covenant never even tried to convince me that the people were worth my emotional investment.