2 of your 3 are elseworlds stories, so if we are talking elseworlds I would also throw in Alex Ross’ Justice, which is a fun comic.
But keeping it in continuity, I’d put Mark Waid’s run clearly at #1. It has such classic stories as Tower of Babel and Divided they Fall. It’s a solid and classic run top to bottom.
For most underrated, I’d go with James Robinson’s much maligned JLA run. People tend to dog on it a lot, but it’s one of my personal favorites because it is so unconventional. The lineup was Dick Grayson as Batman leading a team that included Supergirl, Donna Troy, Jade, Jesse Quick, Starman, and Congorilla. They fight The Crime Syndicate and Eclipso in that run, so it is legit threats. It’s bonkers crazy and amazingly fun. I love it.