Reading PDFs is one of the main things I do on my iPad. There are two apps that regularly get recommended as the best in this area. PDF Expert is one. GoodReader is the other. Both have strengths relative to the other.
I personally choose GoodReader as it has excellent file storage options built in. With GoodReader you can have a two page view, including two different PDFs side by side, or even two non-contiguous pages in the same document if you want to cross-reference or compare info.