The majority 95% + of the interpreters (guides) at Northern Tier use jungle boots, as some one previously posted you can get them from the Norther Tier website, I think they are in the $35 range, not bad when most people going to philmont spend 3-5 times that on boots. you can also take some old backpacking boots and drill holes in the sides or live with sloppy feet the whole trip, it is really not that bad.
In response to the previous poster, you would be hard pressed to find an Interpreter who would let you pull loaded canoes up on to the portage. There are some portages where there is water deeper than calf deep as well. If you are going through Northern Tier, you would need knee high boots or more if you wanted dry feet on a portage.
Happy Trails