Being so close to the equator, which is just south of Singapore, the regions has pretty much the same tropical weather throughout the year with temperatures of about 25°C at night and 30°C during the day. Essentially there are 2 "seasons", the wet season and the not so wet season. Travelling is pretty much possible throughout the year, only the islands along the eastcoast of the Peninsula like the Perhentians shut down most of their operations during the monsoon season from November to mid February. Sarawak and Sabah in the Malaysian part of Borneo also receive substantial amounts of rain between October and March.
Even though the main travel route through Malaysia (Singapore, Melaka, Kuala Lumpur, Penang) also receives more rain from November to February, travelling is not effected. It just means you have bring an umbrella along and enjoy a Kopi or Teh Tarik somewhere dry if the rain gets too strong. Usually, the rain will be over after about 1 hour.
The peak travel season is May to September. The island of Langkawi at the west coast receives most visitors from December to March, when the island at the eastcoast are mostly shut down.
storm clouds coming in, Perhentian Islands