Spain is proud of her heritage, and many (not all) of the diaries of the early explorers have been published both in their original form and in modern Spanish.
The only exceptions are documents around the time Spain was finally unified prior to the muslim expulsion. Those libraries remain in the families of the nobles who experienced (and funded) the history.
My favorite library/book store for Spanish history and documents from the age of exploration...
Madrid, not far from the Palacio Real, and from the prettiest McDonalds you'll eve see...
http://www.casadellibro.com/secciones/seccion/0,,1,00.html?codigo=1