I recently came across a really marvelous online resource on Amazonian languages, the Biblioteca Curt Nimuendaju (http://biblio.etnolinguistica.org/). This open access site makes available for free download in PDF format numerous hard-to-find linguistic works on Amazonian languages and ethnographic works on Amazonian peoples.
The focus of the collection to this point is on Brazilian Amazonian languages, but there are also works available on languages spoken in other parts of Greater Amazonia, and in some cases, in other parts of South America. The site is continuously adding new materials, so I expect that their coverage will expand over time. Interestingly, the organizers offer to locate and add specific works if visitors request them. So if the works you want are not available on the site, there is hope that they could be added.
Here is sampling of works that the Biblioteca currently has available online:
Adam, Lucien. 1902. Le parler des Caingangs. Congrès International des Américanistes (XIIe. Session tenue a Paris en 1900), p. 318-330.
Crowell, Thomas H. 1977. The phonology of Boróro verb, postposition, and noun paradigms. Arquivos de Anatomia e Antropologia (Instituto de Antropologia Prof. Souza Marques, Rio de Janeiro), 2.159.178.
la Grasserie, Raoul de. 1902. Contribution a l’ètude des langues de la Patagonie: vocabulaire Pehuelche. Congrès International des Américanistes (XIIe. Session tenue a Paris en 1900), p. 339-354
Lafone Quevedo, S. A. 1902. La lengua Tacana de la región del Rio Madre de Dios (Bolivia). Congrès International des Américanistes (XIIe. Session tenue a Paris en 1900), p. 331-337.
Larrañaga, Dámaso Antonio. 1923. Compendio del idioma de la nación chaná. Escritos de D. Dámaso A. Larrañaga, tomo III: 163-174. Montevideo: Instituto Histórico y Geográfico del Uruguay, Imprenta Nacional
Rivet, Paul. 1924. Les Indiens Canoeiros. Journal de la Société des Américanistes de Paris, n. s., tome XVI, p. 169-181.
Amazonian Linguistics 