So, what would the Americas look like here without the Paleo-Indians but with the later waves of migrations still around?
Interesting topic. There was a timeline based on a similar premise called Empty America, though I'm pretty sure that the other two waves of expansion didn't happen in that scenario.
I'll limit my speculation to languages and migrations, since I'm not too caught up with North American megafauna. I don't think a lot of species would survive into the Holocene, regardless of humans.
Between 6000 BCE and 4000 BCE, the Na-Dene quickly expand throughout the continent, with Proto-Tlinglit speakers expanding south, wedged between the Pacific and the Rockies. Proto-Eyak-Athabaskan can expand through the interior (like Haplogroup B2 did), spreading east. The Paleo-Eskimo expand throughout the Arctic, likely expanding further south via either the St. Lawrence or the Eastern Seaboard. I could see them getting everything east of the Appalachians. Central and South America are colonized by Tlinglitan speakers via the West Coast. Another possible migration route could be island hopping via the Caribbean, possibly by Paleo-Eskimo speakers. This migration could expand into the Orinoco, later reaching the Amazon via the Casiquiare Canal. The Andes could serve as a barrier between the two peoples in South America.
This is all assuming the main branches had diverged in Beringia, though if not the case, similar linguistic developments might also happen in this scenario. Another postulate in this suggestion is that the Paleo-Eskimo spoke a Dene-Yeniseian language, though it's highly likely.
Next up, we have the Eskimo-Aleut. They migrated into the continent around 2000 BCE (potentially much later, due to possible Eskimo-Aleut loanwords in Northern Tungusic languages), via the Aleutian Islands, so I can see this also happening in this timeline. I don't see any major changes happening with them, as they had a technological advantage over the Paleo-Eskimo, though this could potentially be butterflied away. In that case, they stay a small language family in far western Alaska.
The Vikings could settle Labrador and the Maritimes, potentially migrating into the Great Lakes via the St. Lawrence. They can also migrate south along the East Coast. However, I don't think this would happen in rapid succession, as Viking settling wasn't too intensive. I could see a scattered pool of Vikings in North America by 1500. They could also introduce diseases into North America, depending on if and when they lose contact with Europe.
I can't see Polynesians getting too far, but they can settle along the coast of South America. It'll be interesting if they introduce agriculture to the natives, though it's probably too late to matter.
Speaking of agriculture, if they develop farming or not is up to the TL writer, though they already have a disadvantage of having considerably less time in the continent than the Paleo-Indians had in OTL, and even then it wasn't a lot.