All good advice above and some great suggestions. Having been born and mostly raised on the Island (Duncan, Cobble Hill, Port Hardy, Victoria), one place that's missing from above that I'd put at the top of my list would be Ladysmith. Nice town and you should be able to find what you are looking for your budget, even acreages if you head out towards Yellow Point or Saltaire. Centrally located with easy access to both Nanaimo (ferries and more importantly Harbour Chandler!) and Victoria (ferries), and easy to get across to the West Coast - Port Renfrew via Lake Cowichan or Port Alberni (or farther north) off the Island Highway. Plus you are close to protected waters and the Southern Gulf Islands are on your doorstep - great place to explore in the summer and for your son to learn to boat when he starts heading out on his own.
Probably not the best from a pure fishing perspective, but good prawning and crabbing, decent winter fishing, Gabriola / Porlier in the spring and summer and you could still run across to fish the Fraser in the fall. Sooke would be ok for fishing as well, but driving the Sooke-ahala regularly and dealing with Victoria traffic every time I wanted to go to Trotac would put me off, and much more of a trek to go up Island or to the mainland. For the best fishing you're going to have to go to the west coast, or very north island (Port McNeil/Hardy), but you're trading off quality of schools and access to services. I'd definitely budget to have a truck and trailer (if you don't have one already) to hit up those places - should have lots of place to store them on your new acreage!
Cowichan and Comox Valley's would also be on my short list, but you're likely going to be further from the water in the Cowichan for your budget and Comox area is a bit too far up Island for my preference if you plan to travel to the mainland or through YVR regularly.
Generally, the schools in the central island (Comox - Cowichan) are will be better than the more outlying places - anot. Great fishing in Port Hardy and cheap real estate in Port Alberni, but I wouldn't want to send my kids to school in either if I had the choice (just my opinion from having gone to school / uni in and opinion from friends in the places above). Check
http://britishcolumbia.compareschoolrankings.org for the Fraser Institute's school rankings (FWIW).