In Thor Heyerdahl's book, Kon-Tiki, he has the belief that the peoples of South America settled Easter Island, Pitcairn Island and all of Polynesia. Now, however, modern historians have mostly rejected this view. But the Madagascans came from Indonesia, and the Vikings reached Newfoundland, so it seems entirely plausible that the Polynesians could have come from South America. So, where did the Polynesians come from and why has the South America theory been largely discounted?
Why couldn't the Polynesians have come from South America?
Linguistics, for one. As you said:
But the Madagascans came from Indonesia
Let's forget about Indonesia for a second because that's not really the whole story. The important part is this: Malagasy (the language spoken in Madagascar) is a Malayo-Polynesian language.
If we look at the language, we can say that the Polynesians didn't come from South Africa because we can trace the languages back through time to find that common ancestor between Hawai'ian, Malagasy, Tagalog (Philipines) and Atayalic (Taiwan).
The reason modern historians have rejected Heyerdahl's view is because there's no evidence to support it, and a huge amount of evidence to disprove it. In addition to linguistic evidence, there's also been genetic testing and a good deal in the archaeological record to support the Polynesians as originating from Southeast Asia, either Taiwan or mainland Southeast Asia, and spreading from there through to their current range of Madagascar to the East Pacific.
The reason Indonesia is significant to Madagascar isn't that it was where the Malagasy people came from, but rather that the cultural similarities are significant. Since the 80s at least, mainstream social sciences have been on board with these similarities as being significant, and a lot of what you see in places like Hawai'i are not that far from what you see in Aboriginal villages in places like Taiwan.
I'm going to hope /u/l33t_sas shows up to provide some more details, because he'll do this justice better than I can. But the short of it is, there's simply no evidence to support a South American origin, and all the evidence to support a Southeast Asian origin.
the Madagascans came from Indonesia, and the Vikings reached Newfoundland, so it seems entirely plausible that the Polynesians could have come from South America.
The Malagasy did come from Indonesia, specifically Borneo but I don't see how that makes it plausible that Polynesians came from South America except in the vaguest sense that they're both one island being settled from a distant homeland. Actually the Malagasy and Polynesian languages are clearly related, all being Austronesian languages ultimately descended from the same ancestor (c.f. Maori maso and Malagasy mata 'eye'; Maori talinga and Malagasy tadiny 'ear'; Maori ate and Malagasy ate 'liver'; Maori rua and Malagasy roa 'two'; Malagasy mate and Maori mate 'to die'). So if you are claiming Polynesians are from South America, you are also claiming that Malagasy, Indonesian, Formosans, Filipinos, Micronesians, Vanuatuans, etc. are too or if not that Polynesia was settled by South Americans whose languages were supplanted by modern Polynesian languages without a trace. Both are of course very implausible even on the face of it and certainly modern genetics can prove that the Polynesians are closely related to other Austronesians.
In historical linguistics, it is taken as axiomatic that the common ancestor of languages in a family is likely to be found in the area of greatest diversity. This is because we assume (even if not necessarily always the case) that languages have been spoken continuously in the area since speakers of the ancestor (or proto) language first moved there and thus have had more time to diverge from one another. For Polynesian languages, the area of greatest diversity is in the west, near Tonga and Samoa. Archaeological evidence corroborates this, with dating methods suggesting Tonga was the first island in Polynesia to be settled, around 2800 years ago. This also fits with the fact that Fijian and Rotuman being the closest relatives to Polynesian. Similarly of all the Oceanic languages (a group which encompasses the languages of Polynesia, most of Micronesia and much of island Melanesia), the area with most diversity is north of New Guinea, in the Bismarck Archipelago. We can also see that the Lapita Culture who we know from archaeological remains first settled Tonga and Samoa, has its earliest settlements located in this area. Continuing this, of all the Austronesian languages (Oceanic, Indonesian, Filipino, Malagasy, Chamic, Formosan, etc.), the greatest diversity is found in Taiwan. On the small island of Taiwan, the Austronesian languages there are more different from one another than they are to most other Austronesian languages. All of this paints a picture of an original settlement in Taiwan, probably from what is now the coast of Mainland China, which spread southwards through the Philippines, then west through the Indonesian archipelago (eventually to Madagascar) and east through Sulawesi and the Malukus, the north coast and islands of New Guinea, continuing through the Solomons, Fiji, Tonga and eventually out to Rapa Nui, Aoteoroa (NZ) and Hawai'i.
There is absolutely zero evidence for the South America theory and there wasn't any even back in the 40s when Heyerdahl proposed his theory but the fact that he stuck to it through the 60s, 70s and 80s despite the rapidly growing repository of linguistic, archaeological and eventually genetic evidence against it is a testament to what a hack he was.