Why are clouds black in colour when it is raining?

Clouds are white because the light emitting from the Sun is white. As light passes through a cloud, it interacts with the water droplets and ice crystals, which are much bigger than the atmospheric particles that exist in the sky.

These bigger water droplets and ice crystals, within a cloud, scatter all colours of light almost equally and with the same effectiveness, which means that the scattered light interacts and combines to generate a white colour, so making the clouds appear white. On the other hand, the smaller molecules of air scatter blue light more strongly than other colours giving the impression that the sky is blue.

Cloud bases often seem grey or dark as a result of the same scattering that makes them white. 

When clouds are thin, they let a large portion of the light pass through itself and appear white. But as it gathers more water droplets and ice crystals it gets thicker and denser due to which scattered light is sent back (reflected) upwards, or out to the sides of the cloud. This results in, less light penetration through cloud, making the top and side of the cloud whiter than the base, which receives less light. We perceive this as grey or almost black cloud.

The higher the height of a cloud, the greyer/darker its base look. The top of clouds gets a constant source of white light, due to which they always appear white. 

Although, there is also another reason why we see dark clouds from time to time. It happens when there is another cloud overshadowing it.