If you like cafe hopping, city exploring, and commercialized villages I would recommend Bali.
If you are looking for the authentic Indonesian villages, untouched corals, small fishing village on the coastal with no restaurants or coffee shop, then I would recommend Raja Ampat.
In Raja Ampat, I would recommend to stay around a resort in Waisai, rent a scooter checkout the city (small), take a boat to Kri island and visit the local village there, take a boat to explore the crystal blue lagoon, snokel at the Samdarak Jetty (best spot in r4). There is also bird watching, and dolphin watching.
If you are looking for the authentic Indonesian villages, untouched corals, small fishing village on the coastal with no restaurants or coffee shop, then I would recommend Raja Ampat.
In Raja Ampat, I would recommend to stay around a resort in Waisai, rent a scooter checkout the city (small), take a boat to Kri island and visit the local village there, take a boat to explore the crystal blue lagoon, snokel at the Samdarak Jetty (best spot in r4). There is also bird watching, and dolphin watching.