iBooks is, imo, the best pdf reader for iPad at the moment. It is fast, well implemented and you can read ePub & PDF files without switching apps.
The only problem is that the default way of loading PDF files into the app is rather unpleasant (yeah, I am referring to the 'iTunes sync' procedure).
So here's what I do when I want to read a PDF file in iBooks.
Disclaimer: The following steps require that you install Dropbox (which is free and awesome) both on the device that hosts the pdf file and on your iPad.
- Move the file to your Dropbox folder.
- Open Dropbox for iPad and select the PDF file.
- You will notice the following icon in the upper right corner
- Tap on iBooks and the PDF file will be copied to your iBooks app!