(Actually Zune, it has been out :/ Just not in English)Anyways, Whirl Islands are in the game location as they were in Silver/Gold.Crystal. They should be right next to Cianwood City, Route 41. If you there for Lugia, You will need a Silver Wing to find him.
Lugia will be available after you obtain the Silver Wing, which you obtain after defeating Team Rocket in the Radio Tower. On Heart Gold, you obtain it in Pewter City.