Lord Vishnu in his Krishna Avatar was depicted black as he had a dark skin. However, a large number of images of the Lord show him to be of blue colour instead of black. This displays the shade of His aura that had tints of blue.
On other hand, some believe that since Lord Vishnu is all pervasive and omnipresent, He is shown as blue to depict that He is omnipresent and infinite like the sky. In Vedas and Puranas, Narayana is depicted as having divine blue shades of water filled clouds and has a lotus and Shankha in His hand.