The Whitsundays are a bit odd because many of the islands you see in photos are islands that can be visited for the day by boat (Whitsunday Island for example) rather than being able to stay on them.
Hamilton Island is pretty much the hub for everything because it has an airport, there are also self-contained resorts on Hayman Island, Daydream Island and Lindeman Island.
Hamilton Island is a resort island, which means that all accommodation on the island shares in the facilities across it (i.e. all the pools and so on). Everyone gets around by golf buggy. On the plus side, it has more choice for restaurants, and all the day trips and boating will be available from there. On the downside, it doesn't have the white sands and blue water that you see on Whitsunday Island.
Definitely don't go during cyclone season though, it's not a lot of fun in the rain.