Phuket Ferry :
Phuket really just has two seasons, which are known as "high season" and "low season" (or "green season"). During the low season months (May- September), boat numbers are reduced. During the high season (October - April), boats to the surrounding islands are increased so you will have some more options.
Ferry Samui :
There are three distinct weather seasons on the tropical island of Koh Samui: the dry season (December until February), the hot season (March until August) and the rainy season (September until November).
Bali Ferry :
Bali actually has a variety of tourist periods, notably around the Balinese New Year, 15 December - 15 January, and 1 June - 30 September. During these high traffic periods, boats to the surrounding islands are increased so you will have some more options. The quieter periods are between 16 January - 30 April and 1 October - 14 December historically.