There's a video at
http://youtu.be/ayAcdHuI5hw?t=7m25s showing a guy using various PDF readers including ezPDF on a rooted Nook, to give an idea. The last of them, the Mantano Reader, seems pretty good, if the OP could have a look at that. Repligo is another one which is mentioned favourably on the Nook forum.
Edit: I'm not sure which of those are accessible at the moment.