Kindle 2 or Nook 3G
The term "most books" is hard to define as well. Does the Amazon store have more books then the B&N store? Yeah, usually. This isn't scientific, but a quick search says Amazon has 417,650 Non-fiction books (117,000 which are history) and B&N says 17,399. There is no way to know what is actually in those numbers though and I wouldn't forget that you can add books purchased from other ebook stores (Kobo/Borders, ebooks.com, Sony,etc) onto the Nook that you cannot put (easily, sometimes legally) onto the Kindle.
The only thing I would suggest is find a handful of books you are interested in and do a search on the stores and see what comes up.
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The biggest thing that is going against me is the browser on the nook needs wifi where as the nook doesn't.