Generally, the best time to travel is from the middle of December to the middle of May (off-season for typhoons). It's hot all year round. The water is warm and no wetsuit is needed.
Basically the only way to get to the Philippines is by plane. Manila and Cebu are the only major entry points. There are flights between the Philippines and plenty of Asian cities, Australia, New Zealand and the USA. There are also flights between Davao in Mindanao and Manado on the Indonesian island of Sulawesi. The island is really small, 1 km wide and 7 km long. You can cycle around quite easily or hire a dirt bike to see the island. The local transport is a bicycle with a side cart. These are everywhere and are really cheap - don't take the first price offered. Crocodile is located at the north end of the island.