If you are looking the Ely area check out Moose Track Adventures.  They are right on Farm Lake (BW access) have some really nice cabins.  Good people, too.  Look at their website and see if that is what you have in mind.

On the Echo Trail, I have heard very good things about the Fenske Lake cabins, but we haven't stayed there (yet.)

On the Gunflint, I think it is hard to beat Clearwater.  It is such a beautiful lake with direct BW access, and they have wonderful cabins with docks right on the lake.  Each one seems to have a bit of privacy, too.  But there are lots of other cabins available, too, all along the Gunflint.  We have stayed at the Little Ollie Cabin at Poplar Creek and enjoyed that, but it is a large cabin.  I believe they have a smaller one also.  They are more secluded than some, lake nearby but not really on the lake.  We also rented a cabin at Nor'Wester once, which is right on Poplar Lake.  It was a nice enough cabin, not fancy, had a dock right on the lake, and there was a good swimming beach nearby.  

Just a few suggestions.  I am sure you can find more if you keep looking.