First let me say that I'm NOT going to tell you where the best places are to canoe camp on Isle Royale.  Read on, however, for some useful info:

Why I like canoe camping on Isle Royale
Unlike canoe camping in Boundary Waters or the Canadian north woods, Isle Royale has no long rivers to run, and no trips of a hundred miles or more that are possible.  What Isle Royale offers, though, is mostly uncrowded canoeing, a wide variety of scenery, from inland lakes to sheltered Lake Superior bays, to some exposed Lake Superior shoreline, and the opportunity to combine canoe camping with day hikes and short backpack loops.  Because the canoe country of Isle Royale is fairly small, it's a great place to make travel from campsite to campsite a small fraction of your agenda; go for quality rather than quantity, and spend more time exploring the trails, fishing, playing naturalist, and generally taking it easy.

Canoe camping opportunities
The most common canoe camping trips people take on Isle Royale are
1.    Rock Harbor to Lake Richie to McCargoe Cove to Belle Isle to Duncan Bay to Rock Harbor loop (in either direction)
2.    Rock Harbor to Lake Richie to Siskiwit Lake to Chippewa Harbor to Lake Richie to Rock Harbor loop (in either direction)
3.    Chippewa Harbor to Lake Richie to Siskiwit Lake to Chippewa Harbor loop (in either direction - involves transportation to Chippewa Harbor via the Voyageur)
4.    McCargoe Cove to Belle Isle to Rock Harbor (or reverse, but best to start at McCargoe Cove).  This trip utilizes the National Park Concessions' MV Sandy Tour Boat (which will take canoes on its run to McCargoe Cove for the Minong Mine Interpretive Tour), or the Voyageur (which will stop at McCargoe Cove on its clockwise trip around the Island from Windigo to Rock Harbor).
5.    Siskiwit Lake/Lake Richie/Chippewa Harbor/Wood Lake/Siskiwit Lake loop, accessed at Malone Bay.  Requires transportation to Malone Bay, usually by the Voyageur.

Other options include:
1.    Windigo to Beaver Island, Grace Island, or some shoreline areas north or south of the west end of Washington Harbor.  However, note that rough seas can be frequent outside the shelter of Washington Harbor, and that no camping is allowed on offshore islands except at designated campgrounds.
2.    Rock Harbor (the long harbor, not Snug Harbor, where the lodge and Rock Harbor Campground are located).  This is a nice option for those who desire zero portages.  However, you won't do much wilderness canoeing, and you may have trouble getting into campgrounds such as Merritt Lane, Tookers Island, and Caribou Island, which are frequented by powerboaters.  Rock Harbor is also subject to high winds and waves, especially if the wind blows straight down the harbor in either direction.
3.    Tonkin and Conglomerate Bays (accessed by Middle Islands Passage from Rock Harbor).  These are sheltered bays where camping is permitted, and the distance from the sheltered waters of Rock Harbor is relatively short.  The Park Service once had a campground on Conglomerate Bay.  However, beware that one can be stranded in those bays by high winds and waves for a day or more if high winds from the ENE to east to south come up while you're there.

Blake Point
Many canoeists making a trip around the northeast end of the Island consider paddling around Blake Point to avoid the Tobin Harbor to Duncan Bay portage (and potentially also the trivial Duncan Bay to Five Finger Bay portage).  There are two reasons to consider NOT paddling around Blake Point.  First, the difficulty of the Tobin/Duncan portage is overrated.  While it has very steep spots, it's short enough that with a couple of rests, almost anyone should make the portage without difficulty.  Besides, why not  take a break at the Greenstone Ridge Trail at the high point of the portage, make the easy hike to the spectacular view at Lookout Louise and back, and then continue on with your canoe?  Second, winds and waves on the northwest and southeast sides of Blake Point are almost always different, and you may not know how bad it is on the opposite side of the point until you get there.  While the southeast side provides some protection in Merritt Lane, the northwest side offers no safe harbor for more than a mile west from the point.

Rock Harbor to Chippewa Harbor (and beyond)
If winds and waves are predictable and will be minimal, the trip from Middle Islands Passage to Chippewa Harbor (or vice versa) can be easy, and for much of the way there are places to land.  The trip takes less than 3 hours in good conditions.  However, wind and wave conditions can change conditions can change very quickly on Lake Superior, so the trip should only be attempted under ideal conditions (such as when a high pressure area is cresting over the area and no thunderstorms are predicted).  Travelling west from Chippewa Harbor to Malone Bay and beyond involves the same risks, only moreso.

McCargoe Cove to Pickerel Cove
This often-canoed stretch can easily have waves 2 feet or higher, because it is totally exposed to a north or west wind.  Wind and wave conditions are often not obvious at McCargoe Cove Campground, so I expect many a canoeist has set out from McCargoe Cove bound for Pickerel Cove or beyond, only to encounter high winds and waves at the north end of McCargoe Cove.  Then the decision must be made to wait it out (which could take hours or even a couple days), try to get a site at Birch Island (which may be full), or return to McCargoe Cove and try again on another day.  To minimize the risk of having to go back and forth in McCargoe Cove, checking out wind and wave conditions in the Big Lake, I recommend getting a backcountry permit to camp on the northwest side of McCargoe Cove close to the mouth of the cove.  You may not want or need to use the permit (getting a backcountry camping permit doesn't mean you can't stay in designated campgrounds), but if the scenario described above exists when you reach the north end of the cove, at least you have another option.

Lake Superior is almost always cold!
Even though you've probably been told this before, it can't hurt to emphasize that Lake Superior seldom gets warm.  Mid-summer temperatures just a short distance off shore are usually in the 40's and can be in the 30's if strong winds have brought cold deeper waters to the surface.  Always be aware of this, and consider that the chances of surviving a one mile (or even half mile) swim in such waters, even with a life jacket, could be very low.  Best bet is to stay as close to shore as possible, but far enough out to avoid submerged rocks.

Weather radios and MAFOR
MAFOR weather forecasts are available at such places as Rock Harbor and Windigo Ranger Stations, but I always carry a weather radio when canoeing at Isle Royale.  Forecasts available on weather radios are more detailed, are always available and are constantly updated in changing conditions.  On the south shore of the Island, the station at Houghton, Michigan can be received, while on the north shore, the Thunder Bay, Ontario station can be heard.  There are places in the inland lakes where it is difficult to get either station, but with the exception of Siskiwit Lake (which can develop very large waves), one can't get too far from shore on those lakes, and they tend to be warm in summer.  Except on ridgetops and at the extreme ends of the Island, you will be unlikely to receive both the Houghton and Thunder Bay stations.

Circling Isle Royale by canoe - very dangerous and not recommended!!!
Kayakers sometimes circle the Island, but I would NOT recommend it in a canoe, even perhaps in a covered canoe.  Under ideal conditions, the south shore could be done, but from McGinty Cove to Little Todd Harbor on the north shore there are essentially no harbors, and the shore is steep and rocky.  Even kayakers will only run this stretch in ideal conditions.  Almost no canoeists even attempt the shoreline from Little Todd Harbor to McCargoe Cove, due to its exposure to strong west and north winds and a shortage of landing spots in places.

The open waters of Lake Superior, except for short stretches like from McCargoe Cove to Pickerel Cove and then only in ideal conditions, are for experienced canoeists only.

Getting off and on the Ranger at Mott Island
While most park visitors using the Park Service's Ranger III to access the Island will get on and off at Rock Harbor (Snug Harbor), canoeists and kayakers may also get off and on at Mott Island, where the park headquarters are located.  For those heading west to Moskey Basin and points west, this saves a couple hours of padding, plus you get an earlier start (by an hour or so) than you would if getting off at Rock Harbor Lodge.

A few cautions, though:
1.    Make sure you and your gear (including your boat) are tagged for Mott Island ("Mott") before you leave Houghton; you won't haved the option of changing your mind once the Ranger III is underway.
2.    There is no place to camp on Mott Island.  So, if you get to Mott and Rock Harbor has 3 to 4 foot waves, you might want to reconsider getting off there.  You'd need to talk to a Park Service employee on the boat before arriving at Mott.
3.    If you plan to get on the Ranger III on its way back to Houghton, consider the possibility that rough seas can make it difficult to reach Mott Island at times.  Sudden storms or unexpected high waves may make it difficult to make the boat on time if you don't allow lots of extra time to get to Mott.  If you don't make the boat, they won't wait for you, and you'll be forced to paddle on to Rock Harbor and get the next boat back that has space for you and your boat(s).

Canoe Campsites
See my backpacking page for info on canoe access campsites.