As far as BGP goes, Halabi's _Internet Routing Architectures_  is pretty much considered the "bible". It's really old nowadays but it covers BGP4 (the current version in use) and not much has really changed.
I'm sure some of the newer BGP books are excellent as well but I can't personally recommend them as IRA and the (old) CCNP BGP book are all I've ever read/used (while preparing for the CCNP certification and in my day job).
Of course, pretty much everything is covered in RFC 4271  (and updates) although the RFCs can be a bit "dry".
It's probably not the most up-to-date treatment of BGP and Autonomous Systems, but it's pretty good for learning the basics.
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