Can a 1-stop route beat a nonstop route NYC to TYO for me?
Besides things that were discussed previously. NRT has a curfew from 23:00 to 6:00. 23:00-24:00 delayed flights can land.
At 21:00 arrival ANA option would be safe enough to take the train or shuttle. I wouldn't expect customs to be too long/slow at that hour and bags shouldn't take more than 1 hr.
I would prefer taking ANA; however, the AC option actually allows you to utilize your afternoon shopping, roam around town (Tokyo Tower, Roppongi Hills, etc), and of course eat around too (gives 1-2 extra meals in Japan). Of course this is assuming Saturday plans at departure point.