While that's still rather goofy, there is actually some precedent for awfully-late discoveries of primitive tribes in the vast jungles of South America, which was a surprise to me. Here, for instance, is a story on the recent first contact with the Metyktire tribe, previously living in seclusion on a large native American reservation in the Amazon. Even the main tribe of the reservation had enjoyed no contact with the tribe in a long while.
Most fascinating is this note:
Indians were pushed deeper into the jungle by settlers and it is relatively uncommon for the Indian Bureau to come across previously uncontacted native groups. The bureau said that it has learned from other Indians of a few uncontacted tribes in the western Amazon state, where the region's jungle is thickest.
Moura said anthropologists no longer attempt to contact those groups, but instead demarcate the land and wait for them to make contact.
So maybe there's a smidgen of plausibility in the idea after all, were it not for the fact that the Trek writers put Chakotay's find in the much smaller Central American jungles.