Books as a learning tool are an important resource in the martial arts, and while they can not (and should not) not replace a physical teacher and interaction with a training group they do serve as good reminders to build up a training vocabulary and as a reminder of skills to be working on for your art.
In the Bujinkan dojo method, or for those interested in starting to explore our martial art here are a few reading recommendations written by Dr. Masaaki Hatsumi- the headmaster of the Bujinkan martial arts.
Ninjutsu: History & Tradition: A good blend of history, tradition, and basic techniques as an introduction to the martial art. Also good for new students to help build a checklist of terminology, concepts, and skills practiced in the dojo.
The Way Of The Ninja: An interesting book showing the application of the training philosophy. Not so much of a list of techniques, but rather one giant question asked: Can you do these skills? Here (in the book) is what to train on to make it happen.
Advanced Stick Fighting & Japanese Sword Fighting: Explores two important training tools in the art- the stick and the sword.
Ninpo: Wisdom For Life: Training philosophy and many of the starting concepts in the martial arts.