Try the Maine Island Trail. MITA
The trail runs the entire coast of Maine and offers numerous islands for camping. Much of the coast requires good coastal kayaking skills, much of it requires intermediate skills, and a small portion requires truly expert skills. The coast is beautiful and some of the islands are absolutely spectacular.
There are also two campgrounds on Casco Bay Recompence Shore Camping
in Freeport Maine
And Winslow Memorial Park in South Freeport (Dont have a website)
That offer superb coastal camping with wonderful kayaking, but not Island camping.
Acadia National Park also has wonderful kayaking and camping, but is crowded in the summer and the kayaking requires advanced skill. Sagadahoc Bay Campground
in Georgetown Maine has great day trip kayaking and while the campground is nothing to write home about, it's adequate.
Lobster Buoy Campsites (Sorry no website) in Thomaston is another "OK" campground with superb kayaking in Penobscot Bay and the Muscle Ridge Islands, which are wonderful but not much island camping.
Hope this helps.