Ninjutsu is basically a term used to describe a set of skills and abilities used to control ones life force "chakra" and using it as raw energy or manipulating it for use as a weapon.
'Shape manipulation' itself controls the form of chakra, its movement and strength. usually not involving the manipulation of the environment, or rather the elements of it. Manipulation on the other hand is changing the properties of ones chakra, allowing him to control elements, the simplest example would be heating chakra and manipulating fire.
Chakra is the life forces the dwells withing all living creatures. It has two aspects of it, the physical energy generated by ones body, existing in each cell from burning carbohydrates and breathing, and the spiritual aspect of of will power, based on the individuals persistence and perseverance, his determination.