being a resident of Sydney I can't really comment on Melbourne - hopefully a few Melbournites can fill you in about places to shoot whilst there.
As for Sydney, my pick would be Mrs Macquaries Point on Sydney Harbour. From there you'll get the best views of the Opera House and Bridge. The Rocks area and around the international terminal also offer some great vantage points, as does the foreshore around Milsons Point on the north side of the bridge.
Hyde park lights up nicely at night and Darling Harbour / Cockle Bay is not only a great place to shoot but also a great place to quench a thirst and grab a feed as well.
Hope you enjoy your stay