A Modern Method For Guitar (Series)
Often referred to as the "Berklee Books", this excellent three-part series of books by William Leavitt provides music theory, sight-reading, and technical exercises. This is a great place to start.
The Jazz Theory Book
Published by Sher Music Co, the Jazz Theory Book by Mark Levine is a great introduction to music theory for those who already know the absolute basics. Although it does focus on theory as it relates to jazz music, the book contains useful theory that can be applied to all styles of music.