[LoloMo]

Depends how much you have to spend =)
Palawan El Nido is among the top beaches in the world. It's pretty safe now, since that incident a few years back, the government and private sector have beefed up security and according to newspaper accounts, Abu-Sayaf forces have been more than halved due to continuous military operations against them.

Boracay is another one, safest place to be. Its the summer capital of the Philippines haha.
Puerto Galera is another alternative, probably the cheapest of the three mentioned.
If you want to be adventurous, Cebu area is pretty safe. Don't go adventuring in Mindanao area. And check with your travel agent =)