The difference is that Vishnu is worshiped in awe and reverence while the pastimes of Krishna with His pure devotees are very intimate and sweet. Srila Prabhupada compared Lord Vishnu as God in an official mood, and Krishna as God at home — just as a king may be venerated, worshiped and obeyed by all citizens including great ministers, while at his own home the king acts subordinate to his beloved children, while both are the same person, exhibiting different aspects of their relationships. Similarly Krishna becomes subjugated by the intimate loving dealings of His pure devotees, as we see in the Damodara-lila and other pastimes.
The Nectar of Devotion (Ch 21) gives a list of 64 transcendental qualities of Krishna. It is explained that all living entities can have upto 50 qualities in minute degrees of perfection and Lord Shiva upto 55 qualities. Lord Vishnu has 60 of these qualities unlimitedly in their fullness whereas svayam bhagavan Krishna alone has four special unique qualities not manifested even in Vishnu viz. His superexcellent beauty, the attraction of His flute playing, the wonderful varieties of His intimate pastimes (such as childhood pastimes) and His being surrounded many devotees endowed with wonderful love of God.