I am biased but I second Denis, Johnstone Strait is a fun place to paddle and if you enjoy longer trips, the Broughton Archipelago has some great spots. Take a look at http://www.kayakbc.ca
for both rentals and tours in the area. It is worth taking a look at the tour itineraries, even if only to get an idea of what and where to go either with rentals or your own gear.
For lakes, the Sayward Forest Canoe Trail http://www.vancouverisland.com/recreation/?id=176
just north of Campbell River provides a great 4 day loop. Do it by canoe or kayak. There is a great book recently published describing it. "A paddler's guide to the Sayward Forest Canoe Circuit / Michel Gauthier."
There are many other lakes, most with free wilderness campsites around them. Some boat access only and some you can get a truck camper into. If you want to know more, send me a message, I could rattle on forever on what there is to paddle on North Vancouver Island.