It depends.
For those who prefer modding, those who are fans of many computer games (as well as frequent sales), cross-platform multiplayer, quicker and more frequent patches and updates, easier refunds, and achievements, Steam is to go.
For those who prefer to be able to install Civ VI on multiple Macs (and be able to play them simultaneously) and have stability (as in having fewer crashes from third party software), as well as those who detest Steam for various reasons, the App Store version is to go. Note that for Mac users, the use of the App Store is inevitable anways, as it is used for MacOS updates (which means less installation hassles).
Me, I prefer the App Store. I agree with Beetle; I am interested in extremely few computer games and the Steam sales rarely interest me. I would rather trade flexibility for stability.
One more thing Beetle, the App Store version is available.