One of the best ways to see the harbour is to take to the water in a kayak. It's more personal than just sitting on a ferry, and you are able to visit places that the ferries do not go.
It is possible to hire a kayak and go for a paddle yourself, however on some parts of the central harbour you are required to have a licensed guide with you. It can also be quite dangerous kayaking on a busy harbour with many large and fast moving boats whizzing around, especially if you've not kayaked much before or are unfamiliar with the area.
A guide will also know the most interesting and picturesque places to visit, and most will be able to tell you about the history of the areas you paddle through.
There are a number of companies that operate kayak tours in Sydney. They include
Sydney Harbour Kayaks
Northbridge Kayaks
Ocean Planet Kayaking Tours
Natural Wanders
Apart from tours you can also go on regular early morning paddles such as
this one run by Natural Wanders, which is a great way to keep fit.
If you become an addicted paddler you can join the
NSW Sea Kayak Club which runs regular touring, fitness, instructional, and fishing paddles around Sydney and NSW.
Why? A novel way to see the harbour.
