Nope. Carlton is still third. Just because their fans aren't going to games because their team is shit, doesn't mean they have all died. They are still alive. The single best gauge on supporter base is the Supercoach club supporter rankings. Unlike Morgan surveys which survey a few thousand people, this is a defacto "survey" of 300,000 people.
Melbourne have been last for a while now. Young people just refused to barrack for the Dees after the mid 1960's. Carlton have always been a supporter powerhouse.
SUPERCOACH CLUB SUPPORTER NUMBERS (just counting the 10 Victorian clubs)
Collingwood 23,257.........16.33% of Victorians support Collingwood
Essendon 22,866............16.05% of Victorian support Essendon
Carlton 17,497...............12.28% of Victorians support Carlton
Richmond 15,824...........11.11% of Victorians support Richmond
Hawthorn 15,787............11.08% of Victorians support Hawthorn
Geelong 13,836..............9.72% of Victorians support Geelong
St.Kilda 9,595................6.74% of Victorians support St.Kilda
Nth.Melb 8,699..............6.11% of Victorians support North
W.Bulldogs 7,914...........5.56% of Victorians support the Bulldogs
Melbourne 7,121............5.00% of Victorians support Melbourne