If you want to leave no stone unturned in your search for an online digital edition of a book printed in the15th or 16th century, then you need to work your way through the entire list of libraries with digital editions over at Archivalia. It will take days, but it will be worth the effort, unless you get distracted and start looking at books you never existed, in which case it will take weeks or months but be even more rewarding.
Your next-best option is to check the catalogs of the major digitalization projects (see links in the sidebar). If you don't find what you're looking for, however, there are still two places worth checking.
For incunables, try the verteilte digitale Inkunabelbibliothek (vdIB). Its search data comes from ISTC, and it has links to digital editions from Cologne and Wolfenbüttel. (I'd like to see some evidence that the project is still being actively developed, however. With ISTC and GW adding their own links to digital editions, vdIB may be becoming redundant.)
A more general search engine is the Zentrales Verzeichnis digitalisierter Drucke. Its coverage reaches from 1501 to the present, but its focus is on the 19th and 20th centuries. Still, it's turned up some new sources for me in the past.
And don't forget Google; it led me to a recently digitized first edition of Rheticus's Narratio prima, the first printed description of Copernican cosmology, at the Linda Hall Library of Science, Engineering, and Technology.