I agree with searat, Harbron's book is the best place to start... by the way searat, the floor is yours, Cisneros is a perfectly adequate answer. Also, now I know that both searat's de Lazo question and my answer probably came from the same book... plates XIX and XX!
There are some Spanish language web sites that cover the Spanish perspective, but I haven't found much. I have been to the Greenwich and Paris Museums, so I'm loaded with a lot of material for England and France. I haven't been to Madrid yet, so I don't know what might be available in Spanish.
John Millar's Early American Ships includes Spanish vessels from the late 18th century and an interesting summary of Spanish shibuilding in Havana.
Most of what I have comes from translations of Spanish journals and memiors, mostly about the west coast of America and Pacific exploration. Flood Tide of Empire, The Manila Galleon and Spanish Pacific: from Magellan to Malaspina are good references for exploration and development with references to the Spanish Navy. The Hakluyt Society's two volume set The Malaspina Expedition gives some good info on ranks and organization. Herbert Beale's translations of voyage logs generally include good summaries of the differences in English - Spanish navigation conventions (they don't box the compass the same way).
I don't have much on the Spanish view of the Napoleanic Wars. Peter Goodwin's The Ships of Trafalgar includes Spanish ships and Robert Gardiner's three books on frigates (The First Frigates, The Heavy Frigate and Frigates of the Napoleanic Wars) include some drawings and assessments of Spanish frigates.
David Lyon's The Sailing Navy List includes data on captured Spanish ships taken into the Royal Navy.
Otto von Pivka's Navies of the Napoleanic Era gives brief, overall summaries for most participants.
The rest of my material has been accumulated through journal articles (Donald C. Cutter has done a lot of work on the Spanish Navy as it related to California and the Northwest Coast) in the California Historical Quarterly, Oregon Historical Quarterly, etc.
You also might try the San Diego Maritime Museum. There are articles on the Spanish Navy in the Pacific which occasionally shpw up in their magazine Mains'l Haul.
All of these books add up to a ton of money... so I'd establish a good relationship with your local librarian and learn about inter-library loans.