At my university CA: AQA was used as the text for the second course in computer architecture. The first course in computer architecture used this book: https://www.amazon.com/Computer-Organization-Design-Fourth-A....

If you do get around to reading CA: AQA, you can follow along with this Coursera course (it's taught by the professor I had when I took it at Princeton, and he does a great job teaching it): https://www.coursera.org/learn/comparch

Not strictly computer science - but the one textbook that I really liked from my computer engineering degree was "Computer Organization and Design: The Hardware/Software Interface" (http://www.amazon.com/Computer-Organization-Design-Fourth-Ed...). It was surprisingly readable and easy to follow. It covers the design of a MIPS processor from the ground up (ALU, caches, memory, pipelining, etc) and also is self-aware enough to not pretend that x86/ARM don't exist.

If you're willing to pay - this is probably the canonical textbook.

http://www.amazon.com/Computer-Organization-Design-Fourth-Ed...