For me, iBooks is currently the best PDF reader for iPad, but the options for getting PDF documents into the iBooks library are limited.
Here's how to import a PDF document into iBooks, using just the web address (URL).
1. You'll need the GoodReader app, which you can download from the app store (currently £0.59). GoodReader is a great document viewer, but crucially offers file management tools too.
2. Open GoodReader, tap "web downloads" then "enter URL". Type or paste the address (URL) of the PDF document. This will download and be added to the GoodReader document library.
3. Still in GoodReader, tap "Manage files", then tap the PDF document. Tap the "open in.." button and choose "iBooks" from the list of options. The PDF document will be added to the iBooks library.