There are no exact figures for this, because a disaster can be hard to define, and how accurately records are kept varies from one country to another. Also, natural disasters usually occur over a wider area, so wouldn't always be categorised as occurring in one city.
However, for examples of cities which have suffered very high levels of natural disasters, not many have been as unlucky as Port-au-Prince, the capital of Haiti. This city has flooded repeatedly in the past, is often attacked by hurricanes and has several times been seriously damaged by earthquakes, one of the worst of which was in 2010.
Generally, the cities most likely to suffer natural disasters are in Asia. Recently Mumbai in India and Jakarta in Indonesia, among others, have been named as cities more at risk than others.
According to a recent survey, in the US Dallas is the city most likely to suffer a disaster such as a hurricane, tornado or flood, but is not vulnerable to tsunami or earthquakes.