With Populations (Including current team locations):
Sydney - 4,667,283 (SFC & WSW)
Melbourne - 4,246,345 (MVC & MCFC)
Brisbane - 2,189,878 (Roar)
Perth - 1,897,548 (Glory)
(NZ) Auckland - 1,418.000
Adelaide - 1,277,174 (AU)
Gold Coast - 590,889*
Newcastle - 418,958 (Jets)
Canberra - 411,609
(NZ) Wellington - 397,900 (WPX)
(NZ) Christchurch - 379,100
Central Coast - 321,500* (CCM)
Sunshine Coast - 285,169
Wollongong - 282,099
Hobart - 216,959
(NZ) Hamilton - 212,000
Geelong - 179,042
Townsville - 171,971
Cairns - 142,528
Darwin - 131,678
(NZ) Napier/Hastings - 125,300
(NZ) Tauranga - 123,500
(NZ) Dunedin - 119,100
Toowoomba - 110,472
So three biggest would be Auckland, Gold Coast, Canberra (Numbers are from Wiki, so not sure on trustworthiness), I did just use "City lists" so some areas that have more surrounding parts might be smaller than expected (EG. Townsville/N.Queensland)