I love my Nook, but it does seem that Amazon has a lot better selection. I wonder if there's a way to download it anyway?
There are ways to download kindle books to your computer, then strip the drm and sideload them to another ereader... but depending on where you live it may be illegal. It's not straightforward, and you may lose your formatting. Just search for stripping kindle drm. I think it's a calibre add-on.
I know the question of which ereader is settled, but if other people are considering it:
-The Sony PRS-T1 is the best for reading PDFs. I have the previous model, the prs600. It is great for being able to easily load on service books, the ANF/PNF collections, old out of print books, text books, etc. It can also load books from virtually any online bookstore except for Amazon. Other readers can handle PDF, but none of them do it as well, reflowing it so it is readable without having to constantly zoom in and out of a page.
-Kindle gets you access to the amazon library, which is the best for current paid books.
-I would never buy a kindle fire, because it's a low resolution backlit screen, which means eye strain. I do have the kindle app on my iPod touch, which is still back-lit, but at least has a much higher pixel density. So between my ipod and my sony ereader, I'm covered for access to the amazon library, and great pdf handling.