Popes Eye, Mud Island, Chinamans Hat (seal colony), South Channel Fort, South Channel Light, and Hovel Pile are all well within easy reach with an AI and all well worth a visit, I did them often, if you enjoy snorkelling and/or scuba diving, Popes Eye, the seals and South Channel Fort are great sites and more details are on my Google map along with recommended launch sites on the Mornington Peninsula.
http://maps.google.com.au/maps/ms?ie=UTF8&hl=en&msa=0&msid=117867624084150224494.000488d37120dffdd79e7&ll=-38.234135,144.665565&spn=0.126208,0.308647&z=12&iwloc=000488d4552389edcac9e.
Note: Very strong currents and you are crossing the main shipping channel, extreme caution should be followed when sailing within the area of Port Phillip Heads and the shipping channel.I would also recommend trips on the Lodon, Murrumbidgee, Goulburn and the mighty Murray rivers, every inch of them are worth exploration. {Not for the AI (to many tree's) have a paddle/pedal at Blue Rock dam near Moe}, {Lake Colac and the lakes around Camperdown/Cobden}, Burrumpete(Ballarat), Lanacorie weir, Cairn Curran reservoir (both central Vic), Wartook, Lake Fyans and Bellfeild over in the Grampians, check out the lakes around Nagambie, ow Nhillacootee near Benalla/Mansfield and who could forget Lake Eildon, mate anywhere there is water the world is your oyster and Google Earth your best friend.
I know I have missed so many more and a lot of the little secluded town reservoirs/dams are great viewing as they have less human impact compared to some of the larger water reserves. Forgot the lakes up in the Murray Sunset National Park near Mildura, if they are holding water the wildlife can be spectacular (watch out for drop bears though, deadly and thick in this area).