I have been to several places (Sipadan, Thailand, Philippines, Indonesia, Australia) and I think the Maldives is as good as any of them. Each places is different so focus on the attractions there. The coral was badly affected by the El Nino in 1998 and is not as good as some places in Indo or Philippines, and in general Indian Ocean reefs do not have the same level of color as SE Asia. So if you want shallow coral gardens this might not be the best place in the word. Some of the best Maldives dive sites are for advanced divers due to depth and strong currents but you get great walls/drop offs, excellent fish life and good pelagic action. Regular manta sightings, whale sharks, reef sharks, eagle rays, dogtooth tuna, turtles and huge schools of fish. Would rate it higher than most SE Asian sites for fish action.
Of course Raja Ampat is a whole different story but is not easy to get to and land based options are very limited.
As for Maldives in June, you may have some rain and viz might not be the best but you can still expect decent diving conditions. Dive operators tend to know sheltered sites even if the weather is not great. I have dived there in May/June and had 20-30m viz on some days. You might want to try Baa Atoll in June. Hani Faru is one of the best places to see manta rays and whale sharks especially during the SW monsoon. The peak season is from July to September but June should also provide some good manta sightings. There are also some nice reef dives. The Four Seasons Resort in Landhaa Giravaaru is a great place to base yourself from if looking for a land based holiday.