Sorry. I got the two confused. But would the Sapa Inca not eventually recognize the value of Gran Chaco for agricultural purpouses? As I understand the region was never the center of any civilization even though it is exceptionally well suited for agriculture. It would take a lot less effort to farm en masse there than eke a living off out mountainside terraces fed by aqueducts and canals
I happen to live there, in the Chaco. Just to clear up, the Pampas are the most fertile region, and are shown in juanml82's map. The Inca did not came close to those regions, though trade influence is known. The Great Chaco is located north of them, and isn't well suited for agriculture. The soil has too much clay, the western parts are dry and covered with thick scrub (the "Impenetrable". You can guess how easy is to transit it based on the name) and the eastern parts, while most hospitable to agriculture, are mostly swamp. Even today, the main industries are cotton, soy, and ranching all introduced of course. While some agrarian cultures managed to establish a prescence, it is mainly a terrain for hunting and fishing. In fact, the name Chaco comes from "Hunting Grounds" or "Hunting Time" in Quechua.
The Incas actually tried to conquer the Pilcomayo river under Guayna Capác, and they were defeated by the Guaycurú tribes (which encompass a large group of peoples: the Qom, the Wichi, etc.) They had extensive trade contact with the Inca, and probably would eventually be assimilated with the empire, like the Diaguitas in modern Salta and Jujuy. Most assume that the Chaquenian tribes were primitive hunter gatherers and many of them were, but there is evidence of dams, textile industries and monuments, probably influenced by Andenian civilizations. However, they were also notoriously resistant against Spanish and Argentine colonization (a quite ugly part of our history), even in the 19th and 20th centuries (though the inhospitable climate to Europeans may have played part). So, they won't certainly budge easily to the empire, at least not militarily. The Guaranis also had a quite sophisticated culture, and probably some tribes would settle down eventually (though their religion actually encouraged eternal migration in search of an earthly paradise. Quite interesting, in fact.)
If the Inca survive without contact, and extend their dominion to the Gran Chaco, then the Pampas and their fertile soils are just a boat ride away on the Paraná. The Pampas have no history of agricultural cultures AFAIK, so the Inca/Chaquenian/Guarani colonizers will have to introduce that themselves.
An interesting fact is that, as you can see in the image, all rivers on the region eventually end in the Rio de La Plata (this map does not cover smaller ones). So the Chaco, while not hospitable to large empires from what I speculate, could become a center of trade being in a nice central confluence. You can see the Pilcomayo and Bermejo communicate directly to the Incan heartland.
In a TL without contact between America and Europe, I would see that the Incas would deepeen their influence on the tribes of the Chaco, Salta and the Guaranis in Paraguay and Bolivia. Eventually, as the Inca fall, as all empires do, the successor states that they may stablish on those regions will eventually lead the colonization effort through the Paraná. The Pampa's rich soil could support any great empire, and probably would.
I have a book on the Argentine Chaco, if anyone is interested.