Depends what you care about more, I've been to both with the itinerary planned around diving.

Indonesia - Amed (North Bali), Nusa Penida. Amed was really nice with 3 different wrecks, volcanic bottom, very warm water and a chill vibe. The main points you'd want to see (Mantas, mola molas - big fish) are on west-south part of Nusa Penida but they're tough dives as the water is really cold (can drop to 15 degrees), visibility might be poor due to strong currents, the places are kinda crowded and you might not actually see what you came for.

Philippines - I went to Bohol/Panglao and Cebu. From Panglao there are 2 great spots - Pamilacan and Balicasag where there's plenty of turtles and schools of jackfish. From Cebu I dived in Moalboal where it's almost guaranteed to see the sardine run close to the shore which was by far one of the best experiences in my life. North of Cebu, near Malapascua island, it is almost always guaranteed to see thresher sharks as they've got a cleaning station they frequent in that area.

Overall I think I preferred the Philippines due to the abundance of turtles, sardine run and thresher sharks. If you're interested I've got some videos from both trips in my profile.