Well no one knows for certain. As the ninja were a secretive bunch. However we do have clues from our modern ninja brethren. Some say black while others say a deep red ninja uniform. The black would be worn on moonless nights and the red or deep blue would be worn on nights when there wa s a moon or more light.
It is said the red blends in with the surroundings better because it does not contrast with the surroundings as where the black will stand out more.
And then there are some who say that the ninja would wear whatever would help them blend into the enviornemnt or local people.
My best guess would be that the ninja would wear different clothing based on the mission and the time of day the mission was to be carried out.
An example of the different color uniforms: http://www.ninjauniform.org/
For the grandmaster of modern day ninja go to http://en.wikipedia.org/wiki/Bujinkan
Some pictures of modern day uniforms worn:
