“The rarest item is the item you’re actively hunting for” - Every Collector ever
I’ve always sort of considered how rare an item is to be more based on how often you can farm the enemy dropping them vs their actual drop rate. Sure this isn’t accurate for all cases, but it is still a somewhat good indicator.
Limited edition dungeons usually hold the rarest items because the dungeons can never be acquired again (like BNexus), or because their keys/drop locations are only available for a limited time like the Sword of Illumination from the heroic abyss.
But of course you’re probably referring to the non-limited edition content, to which I say, probably anything relating to the UFO and its alien portals. The UFO doesn’t come often, it’s a pretty rare event that only spawns once per realm (and not even guaranteed, feels like he only comes once every 15 realms on average), and both the UFO and all the alien dungeons it drops can drop white and orange bags. Out of all of them, I’m gonna say the Locked Reactor and the 4 Alien Cores are probably one of the rarest items out there that are not limited edition but are still incredibly difficult to obtain under normal gameplay outside of events