The Mekong Delta is pleasant and tropical with a monsoon climate which means that it is sunny for most of the year. The dry season begins in November and goes on until April and the rainy season goes from May to October. As the heaviest rains come around May to October so, in order to be on the safe side, it is better to visit during the dry season as the region is prone to flooding.
However, if you don't mind getting a little damp, the best time to visit the delta on a Mekong cruise would be April, May and June when the rainy season is just beginning. There are many festivals celebrated around the delta including New Year and the Opening Crop Festival. If you are interested in visiting the delta in time for the fruit season April to May is a perfect time.
In short, the best time to visit the Mekong Delta is around late spring to early summer.