Blair and Robertson's 55 volumes covering from before 1521 to 1898 are all online:

http://philhist.pbworks.com/w/page/16367055/ThePhilippineIslands

Also, there is this: http://www.kasaysayan-kkk.info

Happy hunting.

And if you really want to get down to it, many of the old documents are in Spain, particularly in the Archive of the Indies in Seville. Very many have been scanned.

Blair and Robertson and Jim Richardson mostly present transcriptions and translations into English. If you have the Spanish and are willing to wade through the paleography, you can read the actual scanned documents here:

http://pares.mcu.es/ParesBusquedas/servlets/Control_servlet?accion=0

Try searching for Katipunan, for example. Or Juan de Salcedo Manila