Pre-contact "cities" in the Amazon.

[Oerdin]

I find stuff like this fascinating.

https://www.bbc.com/news/science-environment-67940671.amp

Personally, I wouldn't call them cities in any classic sense as they are really just sprawling low density collections of villages but they were relatively close together and did cooperate of communal architecture.  Even if it was just in the most basic form of water diversion projects/flood control, the creation of earth mounds for religious purposes or for people to retreat to/live on during floods or even basic canals so villagers could trade and communicate with each other.

The low density nature of these sprawling "cities" is probably due to the limitations of available agriculture.  The moscovoy duck was domesticated in the Amazon but nothing else, there is evidence of fish farming, manioc(casava) was grown and probably domesticated there, plus there is extensive evidence that sweet potatoes arrived from the Andes region, but other than that it was mostly fruit orchards.  People would clear forrests then plant various fruit and other useful trees as a kind of orchard permaculture. 

They never got out of the stone age and because of the severe shortage of stone it was mostly a bone, wood, and clay age leaving very little physical surviving into the modern age.  Very early explorers did describe large numbers of people living in the region as farmers and hunter gatherers but when the next group arrived 100 years later virtually no people were there. 

Pretty obviously diseases from the old world wiped them out and the remain groups are just the descendents of the few survivors.