Clouds can be a variation of grays, from white to some dark gray, almost black. They are clearly grayscale, so it means they reflect all colours uniformly, but some clouds are whiter than others, so the reflectance varies. What makes a cloud to be darker than an another? Typically rain clouds are darker, is the tone a measure of how much "water" they are carrying?
You are just seeing differently illuminated clouds, as should be clear from this picture of an aircraft flying over a thunderstorm:
Clouds are made of water droplets or ice crystal, which are transparent. When light is incident upon a cloud, it is scattered at the same wavelength (a process known as Mie scattering). This means that it remains of the same color.
Look at this picture of clouds at sunset: they are red because they are scattering red sunlight. The upper part appears more gray-ish because it receives less light. It is clear from the illumination of the clouds that light is coming from below (the upper part is darker) because the Sun's position is low.