If you sync with iTunes on a computer, add the PDF files to the iTunes library on the computer. Then, with the iPad connected and selected in iTunes, set them up to sync in the Books tab, then sync. They will show up in the iBooks app under the PDFs Collection.
If not using a computer, try emailing the books to yourself. When they show up in the Mail app, tap and hold on them for options. Open In iBooks should appear. Unlike the previous method you won't have a backup copy on the computer, so make sure you keep another copy somewhere else, maybe DropBox, just in case.
You can do the same think if you download them in Safari. Tap in the center of the PDF when it finishes downloading and the top right icon (a box and arrow) for the option to Open In iBooks.
I only know two ways to add a PDF book to the Kindle app.
One is to use the
File Sharing feature in iTunes on a computer.
The other involves importing the book to your Kindle library on
Amazon's site. When you do that it will appear in your Cloud library just like any other Kindle book. I've never used it and don't know the in-outs and cautions; so read up before trying.
Amazon.com Help: Kindle Personal Documents Service
As a side note, both the GoodReader and PDF Expert apps will let you bookmark and much more; but if all you want is a reading app they are probably overkill.
