Amos Eaton's journal which covers some of his excursions is in the Manuscripts and Special Collections, New York State Library.  Some of this papers are in the RPI archives, while others can be found in repositories such as Syracuse University and the Pennsylvania Historical Society. 

My particular interest in his botany/geology excursions on the rivers and canals which he conducted for the Rensselaer Institute,  was a famous chance meeting he had on the Erie Canal with the eccentric naturalist, Constantine Rafinesque, which had an impact on the history of botany in the Capital District area.  I have produced a two-part publication on this subject (a summary history and document packet) and will mail the same to any interested subscriber.