I need an ereader application that can be effectively used with textbooks; it should support features like note taking, searching, highlighting, and organizing books of any format (EPUB, PDF).
What are my alternatives?
Google Play Books (GPB) app can do that and very well. It also stores books in the cloud.
But so can iBooks. And the Bluefire app. And Adobe Digital Editions app for android can do that as well. (For .mobi files, the kindle app lets you perform the function). Most ebook reading system can perform the basic functions you mentioned.
The big caveat is IF the EPUB or PDF is DRM free. Still, you can buy the textbook directly from the Apple or Google store and view the book with all these features.
Two additional points:
Many textbook manufacturers don't release or sell DRM-free versions which you can upload directly into the app.
Some textbooks use multimedia which is not fully supported in some of the epub readers listed above. For this reason, sometimes textbooks are sold as "apps" instead of as ebooks which are viewable in a mobile app. If that is the case, you don't need to use an epub reader.
Goodreader for iOS doesn't have epub support.