My gut says ATYCLB as that was my first U2 album and how I got into them. Overtime, my fondness for it has faded, but I can still listen to it and it's soaked in nostalgia for me. I do think there are some pretty good songs on it. Still, those sessions yielded Stateless, TGBHF, Levitate, Love You Like Mad, Big Girls Are Best to name few, which I enjoy.
Out of those 4, I'm tempted to say Songs of Innocence is the strongest album, which has a very strong back half, side A not so much. I also like the b-sides. As many have pointed out, it's got the strongest collection of songs that work together as a whole.
HTDAAB, I don't hate, but too polished and should've been more raw, plus Yahweh is just...yikes (and I actually enjoy Wild Honey).
NLOTH has some really strong songs, but I wish they went further with it. It's decent, but had more potential, so ultimately disappointing. It's those middle three songs that bring it down a bit, perhaps the 2 EPs idea they originally had (Daylight/Darkness) was better.
I guess, I'll say SOI is my favorite for now.
On a separate note, I think NLOTH has my favorite cover art of their 00s albums, but that's not altogether a tough decision for me.