I've used both iBooks and Goodreader for pdfs. GoodReader wins hands-down. You can open it as a disk on your computer and transfer folders direct. It allows you to crop pages, which can give you a larger text-image. It also offers a lot of other possibilities: you can use it as a file-manager, for it transfers files to other apps (such as iBooks).
A big drawback for the moment is the lack of annotation. They say they are working on this. For the moment, when I have a pdf that I wish to scribble on, I send it from GoodReader to iAnnotate and mark up there.