I'm still looking through the various books in my house for a better description (funnily enough, I've got two books discussing shuriken-jutsu, but what I have for knife-throwing more or less boils down to "throw it"), but one major difference I've encountered is that shuriken-jutsu is more likely to use a non-vertical angle. For example, these examples from a Prague Bujinkan school all have a diagonal throw between the shoulder and the opposite hip.
Jōdan uchi 上段打ち – vertical throw from top to bottom
We start in Shizentai 自然体 or Shinzen no kamae 自然の構え position, that means from a common stance. We have a Shuriken 手裏剣 prepared in our right palm, point facing forward. We continue with a left step forward and simultaneously move our right hand to the side of the head in such a way that the blade cannot be seen from a front view. With a rapid twist of right hip forward we swing our right arm diagonally in front of our body so that the right arm “falls” down to the left hip. In such movement the shuriken is released from our hand due to the centrifugal force and flies to its target.
Gyaku uchi 逆打ち – diagonal and horizontal throw
We start in Shinzen no kamae 自然の構え position. We have a Shuriken 手裏剣 prepared in our right palm, point facing forward. We continue with right step forward and simultaneously move our right hand in front of our body over our left shoulder. We rotate the palm outside and with a rapid twist in hips we swing our right hand so that it “falls” down to the right hip. In such movement the shuriken is released from our hand due to the centrifugal force and flies to its target.
A student should always follow the basics which are built upon taijutsu movements. The right hand uses the same movement as during Ura shutō ken 裏手刀拳 punch.
Age uchi 上げ打ち – throw from bottom to top
In this technique, we start in Shinzen no kamae 自然の構え position with a Shuriken 手裏剣 prepared in our right palm, point facing forward. We continue with a right step backward to Shōshin no kamae 初心の構え position where the left arm is stretched in front of the body and the right hand with shuriken is down next to the right hip. Then there is a right step forward with a rapid swing of the right hand diagonally upward to the left shoulder. In such movement the shuriken is released from our hand due to the centrifugal force and flies to its target.
Similarly, this Togakure Ryu video demonstrates more of a frisbee movement.
In comparison, most Western knife-throwing technique that I've seen involves a vertical top-to-bottom movement, done from head to shoulder height (Gil Hibben's style is demonstrated in this video). This is a technique also seen when throwing shuriken, but not as the prevalent method.
Lastly, and this might be more a matter of scale and a difference in intent (shuriken generally being smaller, lighter, and more of a distraction technique, versus knife-throwing where you're looking for more significant penetration with a heavier weapon), but I haven't really seen a knife-throwing demonstration where the motion is primarily a flick of the wrist (versus a full arm movement) whereas that seems to be an accepted technique for shuriken, particularly when throwing several in rapid succession.