Both words are used to show disapproval. If you are accused of nepotism, then you use your position to promote or help the members of your family; it is favouritism based on kinship. The word comes from the Latin ‘nepos’ meaning ‘nephew’.
*Prema got the job because of nepotism — her father is the CEO of the company!
The word ‘crony’ (rhymes with ‘pony’ and ‘Tony’) is used to refer to a friend with whom you spend a lot of time. When you accuse someone of cronyism, what you mean is that the person is using his official position to help his friends.
*Bush and Cheney have often been accused of cronyism.