I've been to both, although Habitat was a few years back. I was just at Sunset Waters last year and liked it much. At one point a few years ago, the same company operated the dive operation at both resorts.
Here's a few points of comparison:
Boat diving: advantage Sunset. Their island location is superior for reaching the best spots on the northwest side of the island.
Shore diving: advantage Habitiat. They are set up like many Bonaire places where you can go down to the dock at any time and jump off the pier. Sunset has a beach/lagoon entry and a longer swim to the reef.
Amenities: advantage Sunset. I liked the all-inclusive plan, and you could eat when you wanted and order from the menu. Nice having the beer/wine/booze included. Habitat plan included a good breakfast, but you'd probably want to rent a car to avoid being confined to the on-site restaurant, which I recall as mediocre and maddeninly slow and uncaring. (Maybe that's changed?).
Sunset is under new ownership after being closed for a while. The new owners are from Chicago and the dive shop owners from Colorado. Everybody there was very nice. Habitat is owned by a Dutch group, but it's been too long for me to know the current atmosphere.
You'll get tired of eating there all week.
