Malaysia is split across two landmasses, Penisular Malaysia and Malaysian Borneo (Sabah and Sarawak), and the best season for snorkeling differs across these locations.
Peninsular Malaysia has an annual monsoon season (from April to October in the southwest, and October to February in the northeast) so you'd avoid these times if snorkeling is on your 'to-do list' for your holiday.
Sabah, Northern Borneo is known as the 'Land Below the Wind' a phrase used by seafarers in the past to describe all the lands located below the typhoon belt, so free from climatic disturbances and typhoons. This makes Sabah a 365 days a year location for holidays with snorkeling offered all year round, albeit the months at the start of the Dry Season (April - June) usually offer the calmest, driest weather perfect for snorkeling.