There is no particular part of the body that is considered to be the cleanest. This is because every part can be contaminated with microbes. However, those parts being least contaminated are the eyes, the internal organs which contain a lot of white blood cells and the insides of the fingernails.
There is no specific part of the body that is free from bacteria. Our skin is exposed in external environment which may have a bacteria. But some people consider our eyes as the cleanest part, since it prosduce salty fluids which cleanses itself.