In terms of ease of access and affordability the best islands for snorkelling at in Sabah are located within Tunku Abdul Rahman Marine Park. The Marine Park which is located in front of Kota Kinabalu is home to five islands - Sapi, Gaya, Mamutik, Manukan and Sulug - and each of them is fringed by coral reefs. The three islands with beaches open to the public offer snorkeling from the beach in a cordoned off area, although the best snorkeling in the Marine Park is to be had from a boat along coral reef sites away from the busy beaches.
For that perfect island getaway experience you should check out Lankayan Island located in the Sulu Sea accessible via Sandakan on the east coast of Sabah. Lankayan offers world class snorkeling right from the shore and with just one Resort located on the island you will feel like you have the white sandy beach and fringing coral reefs almost to yourself. The shallow waters are typically beautifully clear offering easy sightings of turtles, rays, and a range of tropical fish life from the beach.
The dream for non divers visiting Sabah is to go snorkeling at world famous Sipadan. However this it not that easy to do as only a selection of Resorts / Operators will allocate Sipadan permits to snorkelers (most allocate them to diving guests only). One Resort who takes snorkelers to Sipadan is Mataking Reef Island Resort (subject to permit allocation).