Banyan Tree Madivaru is fantastic. Though they don't have over-water bungalows, there are only six huge tented rooms on the island, each with their own pool and spa. It's very private, your butler will organise dinners on the beach for you and you'll get private dive excursions. The home reef is good, but there are lots nearby.
I wasn't crazy about Four Seasons Kuda Huraa. The service is great but it's a big resort and the design isn't normal Four Seasons standard. Apparently Landaa, their other Maldives property, is nicer, but I haven't been there.