Hi,
I would suggest either flying into Airlie Beach (which is on the mainland opposite the islands) or Hamilton Island would be your best bet. Just note that the Airlie Beach airport is actually called Prosperine and it is inland of the actual Airlie Beach townsite. Also if you fly into Hamilton Island and you're not staying on that particular island, or if you're staying on the mainland, you will need to take a ferry back to the mainland (Airlie Beach) anyway.
That said, you can often pick up some cheap flights to Hamilton Island, so I guess your best bet would be to have a look on the websites of the airlines and work out whether it's cheaper to fly to Airlie Beach (Prosperine) or Hamilton Island, on the dates that you want to travel. Jetstar and Virgin Blue often have cheap Sydney - Hamilton Island or Prosperine flights (you may have to connect through Brisbane first), but you could also look at Qantas.
Mackay is further south so flying into there will require a bit of a drive to get to Airlie Beach (I think its about 150km). This map shows the locations of Airlie Beach and Mackay:
http://www.smallguide.com.au/mapqld_whit.html
This site below has some good info about the cost of transfers once you arrive at the airport.
http://www.ozsail.com.au/11191.htm