Queenscliff has some mad beaches for kitesurfing. I've been for a a kite on the beach on the left hand side of the harbour as you look across to sorrento. The locals said it was the first time they'd ever seen kites out there....Otherwise I've heard swan bay is good.
I've kited at St Leonards and I highly recommend it, beach is really narrow so you have to really know what you're doing, be careful when landing and launching. You can get some really clear flat water there too!