I watched most of the Saints game, and I own each guy in a couple leagues. Cooks definitely was the top priority of the defense in most weeks, and Thomas benefited from facing lesser corners quite a bit. I don't think they're particularly close in talent.
I think Thomas is going to be a lot less efficient next year with more attention. He'll also probably get another 1-1.5 targets per game (140s has been the max for NO WRs for the last decade) so I think his production should remain about the same. But there is some logic for his production going down. He'll face more top corners and will have a harder time getting open. I think it's being overstated by some, because some teams won't have their top corner cover the slot, which is where Thomas lines up the most. But some downtick wouldn't shock me.
As for Cooks, I think he's been miscast as a stretch wr in NO. He was deployed all over in college and thrived. I think he'll eventually assume that role from Edelman, which is why I think his targets and production will go up.