Here is an archive that you can browse fleets of ships with names of passengers that traveled from Spain to the Americas. It is under the term "Relacion de Pasajeros:"

Starts on pg2:

http://pares.mcu.es/ParesBusquedas20/catalogo/find?nm=&texto=Relaci%C3%…

My ancestor Joan Angon was on the Flota de 1606 to Nueva Espana.

He traveled on the Navio La Nao Magdalena. Nao is a class type of ship which are characterized by their shape. A U shape in the middle which is same class that Columbus sailed in.

One note is while I was browsing this list of archives I saw one called "Flota de Azogues." I don't know what is that. But after looking it up is is a "Flota de Mercantes." Or Fleet of Merchants.

https://todoavante.es/index.php?title=Categor%C3%ADa%3AFlota_de_Azogues…