Gday Scott
I live nearby in Newport - next suburb in from Williamstown.
My opinion is to scrap Sanctuary Lakes. I assume you will be working in the city? Well the drive from SL to the city will do your head in in peak hour traffic. Plus there is no train line nearby. My mate lived in sanctuary lakes - they have roving security that are "conformity police" - probably have a go at you trying to sail on the lake. Hard to get to the bay from there - werribee, Point cook or altona are the closest bay locations.
As for Altona - it is a kiters paradise, shallow water for a while but out the back it is ok B&J. Handles SW-SE. Plus if your fin is not too big you can sail in an offshore northerly close to the boat ramp - only stay in the shallow water! You can enjoy the smells from the Mobil refinery plus hit the occasional sandbank. Yep you get lots of weed at altona but a local company is turning it into fertilizer so it gets cleaned up regularly. If you believe in sea levels to rise I wouldn't buy there either - it is only 1 meter or so above sea level.
Williamstown - As Red says you have the beach in East - South - West winds. There are some reefy bits to watch out for. Good bunch of blokes that sail out of there. On the yarra side we have the speed track - flat water in a northerly + mid to high tide. A few options. Close to the city.
My preference would be Williamstown or nearby suburbs or the other side of the bay around Sandringham and further south. You will have more sailing choices and better "scenery"

welcome to oz.