I have been canoe camping and fishing for 47 years in Quetico and BWCA and have never seen anyone there with a row boat.  Most people now use kevlar canoes, 50 lbs, which will carry several hundred  pounds of gear.  So you might consider building a wood strip canoe for use in BWCA or Quetico.  Lots of outfitters in Ely MN to rent canoes from.  I hope this helps.

One other thing regarding rowing in BWCA.  When you are rowing, you face the stern, which makes it nearly impossible to see rocks just under the surface.  In a canoe, it is the bow paddler who will spot these rocks and posibly avoid them.

Unless you are a rowing enthusiest or want to sail, I think a tandem kayak would be a far better choice to meet your stated desires.  I agree that the Mill Creek may be a bit small but either the Chesapeake Double/Triple or Shearwater Double would be good choices.  Both designs have a considerable payload and will be significantly faster than a rowed NE Dory even with only one paddling.  A friend has a Chesapeake Double that he has used in the Everglades Challenge.  It has a huge payload and is plenty fast with two paddlers.  His only complaint is that it is pretty wide which makes it hard to get an efficient stroke.  I have a Shearwater Double and love it.  It is smaller and easier to manage than the Chesapeake but has less less capacity (575#) and is probably a bit slower with two dedicated paddlers.  Generally, my flea weight wife and I paddle at 4.0-4.5 mph with little help from her (note her paddling form below).  We did do our first race this spring and paddled 10k in 1:05.  Another advantage of the Shearwater is that the two paddlers are 6.5' apart so you can paddle out of sync and not hit paddles.  Lastly, the Shearwater is megga-stable and could handle some serious rough weather with both paddlers wearing skirts.  I am sure the same could be said for the Chesapeake. 

   If your doing ANY kayaking please learn and practice capsize recovery both you and your son.tipping over in a kayak shoudn't be more than mildly annoying

   Id say go with  the shearwater. Its easier to transport,store,launch and portage.stability is a non issue you'd really almost have to try to  tip that boat over and with a little practice the worst that would happen is you get wet. Its a lot faster paddled. The only advantages of the dory for you would be the abilty to carry more people or gear

   I think you may be asking too much of any one boat. If you want a boat that's versatile -- easy to row, easy to sail, very stable, plenty of payload -- then I think you can't beat the Northeaster Dory. But unless you are Hercules, you should forget about portaging it in the Boundary Waters. Maybe you could manage 1/4 mile with a cart on a level path.

You might be able to portage the Wood Duck double (60 lbs), and it would be a solid boat for virtually everything you describe. The Dory is roomier and more comfortable; the Wood Duck would be easier to paddle.

The Shearwater Double would also be a good choice, unless you think it is a bit too much to portage.

With a young son, you  might be wise to avoid portages and big stretches of open water.

   A collapsable kayak dolly would solve the portage issue ,for that matter something similar could be slapped together for the dory.the trick is to predict what your really going to be using the boat for on a regular basis and get what fits that purpose

   A collapsable kayak dolly would solve the portage issue ,for that matter something similar could be slapped together for the dory.the trick is to predict what your really going to be using the boat for on a regular basis and get what fits that purpose      ps dang that shearwater double looks pretty!

   Thanks for all the advice.  It's all helpful.  I don't have a lot of kayak experience so was thinking a kayak might be too unstable in choppy water, but I think I underestimated them.  As Birch2 said, I might be asking too much of one boat so maybe this is a good excuse to build two (or three).  I think I'll start with one or the other, see what the capabilities are, then build the second if it makes sense to do so.  I also like what Anvil Ed said about being able to see where you're going so I can watch out for submerged rocks and trees.  I don't think I'll do much portaging if I can help it and will plan most trips with that in mind.  Mark N, your wife has the same paddle technique as my son, except he normally has a fishing pole in his hands.

Not practical to portage the yawl or dory. The dolly is good in theory but can be impossible in rough terrain unless it has giant wheels, and how do you transport it in the boat? I agree with Anvil Ed that the best boat for what you're describing is a modern lightweight version of the "prospector" canoe. Mine's a 16.5ft Quessy Odyssée (aka Langford Nahanni, allegedly).

I'm very familiar with kayaks (albeit racing kayaks). I do my canoe camping with my 16.5ft canoe with a flat bottom, low sides, minimal rocker, and aluminum gunnels. Comparing a prospector to a kayak of similar length: 
* kayak is easier to control. Centre of gravity is lower so the boat is more stable.
* Paddling fast in a straight line is is easier and more efficient in a kayak. No J-stroke to learn. You might even have a rudder or "wing" blades.
* Canoe is lighter. At 50lb I can lift mine over my head solo and place it on the roof of my van.
* with yoke can portage solo, kayak has to be carried by two people
* canoe has more versatile seating. Especially with kids it's nice to let the kid at the bow face you while fishing. Also can paddle solo (kneeling in the middle) or with three adults or two adults and two kids, etc.
* canoe is easier to load (no deck, hatches). In conditions where a kayak deck would be necessary to stay afloat I wouldn't go out anyway.
* canoe has a much higher capacity. Mine's rated at 900lb! 
* canoe can be loaded on the stock transverse roof bars on my van. Kayak would require a special rack.

All that being said, we want to expand our horizons to the east coast -- which is why we've just built a NE Dory! Different boats for different trips.

I'd suggest you make some trips in a rental boat to see what suits you. Find out what your style is. Is it worth it to do a short portage to get away from motorboats and crowds? Or do you want the convenience of a Coleman Stove and a YETI cooler? Maybe speed is your main requirement?

Sorry for the long message, I didn't have time to write a short one.

  " I don't have a lot of kayak experience so was thinking a kayak might be too unstable in choppy water, but I think I underestimated them. "

You may not be aware that you have discovered the key to kayak stability. Yes there are suttle differences in kayak stability but it is the paddler's skill  that mostly determines "stability."

Not the boundry waters you may be thinking about, but our Canoe club Commador just returned from Saskatawan (sp?). Where on their 9 day trip they had to portage a few times. The area they were at had a storm this spring. There were lots of downed trees over the trails. A cart would have been useless.

   Thanks for the John and "Grumpy".  I've been thinking more about putting my canoe into use for the camping/fishing part of these trips.  I have an Old Towne canoe that doesn't get much use.  I scared myself this spring when I got blown off a smaller lake and couldn't control it enough to get where I needed to be (back at the boat launch).  I've been watching some youtube videos on canoeing technique since then and now I think it was mostly my lack of skill and understanding that caused that problem.  I'll be taking the canoe out again soon to practice some of the techniques I learned to see if that allows me to maneuver it better in windy choppy conditions.  If so, that will be the boat of choice for the boundary waters and Isle Royale.  Then I think I would build the Chester Yawl just for the fun (and exercise) of rowing, and the beauty of the boat itself.