Hamilton Island and Proserpine are the airports that service the region. Boats depart from adjacent to the airport at Hamilton to many of the Whitsunday Island resorts. Alternatively you can get the bus from Proserpine to Shute Harbour, and out to the islands from there. There are agents that will offer and price inclusive of this transfer.
There are buses from Airlie Beach to Shute Harbour as well, and it is a popular stopping off point. Sometimes standby rates for the island resorts are available there.
Even though it isn't that far of the Queensland coast, access by private boat isn't as simple as you may first think. Hamilton Island has many coral reefs near it and the tidal range is 5.9m. There is a marina call in on Marine VHF radio Ch 68 or telephone 07 4946 8353 but prices start at about $17 per hour or $60 per day 5 June 2011. It makes stopping by for lunch at one of the many restruants a bit less attractive.
Hamilton Island is visited occasionally by cruises. Most must tender their passengers to shore, where they have immediate access to a modest selection of rather nice resort shops and restaurants.