I have a solid list of sights and routes, but am struggling a bit on lodging.
I highly recommend renting a pontoon, or chartering same, to get a much more "up close and personal" look at these magnificent rock walls. We did this a couple of years ago. You can take your time, get right up next to the cliffs in some cases, and even stop at some beaches that are not accessible any other way. We chartered from a guy in Christmas, MI.
Plenty of folks kayak around the area, but the combination of a kayak and Lake Superior scares the crap out of me.
I agree some time in Marquette and Munising (Pictured Rocks) is a good idea. There's a Holiday Inn Express in Munising that is surprisingly nice, with a great view and location. In Marquette, the Landmark is cool but can run pretty expensive. Both the Fairfield and Hampton on the waterfront are good options. Pictured Rocks is well worth the time and one of the great family trips we've taken.
If you want to reach the end of American civilization, there are few better places than the Keweenaw Peninsula. The Keweenaw Mountain Lodge is your best bet up there, but book soon. My guess is the additional jaunt to Isle Royale may not be in the cards, as the seaplane trips are likely booked by now.
Overall, make sure to hit Pictured Rocks, Marquette, and hopefully Houghton and Copper Harbor. And work in a drive on Highway 2, along the Lake Michigan shoreline.
I am not as high on Tahquamenon Falls as most people, but maybe most people are right and I'm wrong.
if you like being tossed all over the place for 5-6 hours.
Lots of lodging options. Punches way above its weight for food. Fantastic outdoor options nearby (see, e.g., Black Rocks).
If you can swing it, golf the Greywalls course at Marquette C.C.
Marquette very nice. Getting more national publicity these days.
Link below, plus my favorite person after fulfilling her flower girl duties in the Sky room.
I stayed and played here many moons ago. Decent location and facilities from what I can remember.
Houghton has the best hotels and restaurants. North of the bridge is more B&Bs. From Houghton you can get everywhere you want to go easily. I have only drank at The Vault Hotel in Houghton, but it looked nice. Everything else in Houghton mostly chains hotels (new Hampton Inn on the water).