The best snorkeling on Perhentian Kecil is at the northern end of Coral Bay or the northern end of Long Beach. Both are similar in the regards of types of coral and fish, and you should see turtles and rays on both locations.
On Besar, Teluk Dalam is the best bay for snorkeling. Sharks are said to frequent the formation of underwater rocks and coral at the westernmost tip of this bay.
Everywhere the water is exceptionally clear and very warm. The islands are one of the best snorkeling sites I've ever seen, and very safe too.