I really enjoyed Nier Automata -- I'd say it's a solid second place -- but it doesn't hold a candle to Horizon: Zero Dawn. The storytelling was superb, and the gameplay was really good too.
One illustrative difference is the side quests: I don't remember a single Horizon: Zero Dawn side quest. Nier Automata's side quests, meanwhile, are almost always tied into the main story or its themes - even if you don't realize it at the time you're doing the quest.
Nier Automata is rough around the edges, but the whole comes together to be greater than the sum of its parts. Horizon: Zero Dawn, on the other hand, is very polished and well-executed, but it doesn't "gel" as well as Nier Automata, nor does it take as many risks.
(SPOILER: You see a circle of metal flowers around Sobek's grave at her home, implying they're GAIA's memorial to Sobek)