I've been paddling and portagin in the northwoods for a couple decades now, and I still haven't figured out what the perfect shoe(s) to pack are. Here are some thoughts. I'm curious what other people think.
Muck boots, Chota, etc. keep your feet dry and happy, and are especially nice when the portage trail is foot deep moose muck, but they're hot, and if you step in water over the top you're screwed!
Chacos, Tevas, etc. are great because you can splash in and out of the water all day, and you don't have to worry about how deep it is, but if you are out of the boat portaging a lot, the straps rub your feet raw, and getting a rock stuck under your arch with a boat on your shoulders, a pack on your back, and 100 rods to go would probably qualify as cruel and unusual punishment. Also, stubbing your toe is a real risk.
Keens and similar are nice since they have a closed toe, but they are also prone to getting rocks stuck in them (though not as bad as Chacos). Being dedicated water shoes, they also don't tear tear your feet up as bad when you're hiking in them wet all day. I think the Newport H2s are my favorite, but I think I could do better.
Anybody ever try a pair of wading boots with just neoprene socks instead of waders?
I was just in Boundary Waters Canoe Wilderness Area and had the same conundrum. I ended up wearing minimalist hiking boots that dry out quickly and clean easily, but the bottoms have good traction for the rocks and roots.
My friends love their Astral water shoes (brewer/Rassler). But they are mostly using them to get to/from the river, and around significant rapids. So they probably aren't portaging the same distances you are... but something worth checking out, given that they love them enough to wear them off the river.
I'll second @circuitmonkey! I love my Astrals for portaging, I've got both the Lowyak and the Brewess and have been really impressed. I use the Lowyaks more for daytripping and if I'm portaging it's my kayak around a rapid I don't want to run. The Brewess are defintely more of the workhorse. I used to be a canoe guide in northern Michigan and wore grippy trail running shoes that dried fast as my portaging shoes back then, so I've always prefered a lighter weight and breathable option.
I did guide a short fishing trip once where we portaged in wading boots and it was pretty clunky, but that could be my personal preference. Plus, it wasn't the foot deep muckiness you mentioned, so we weren't really getting the benefit of avoid moose muck!
Wet foot or dry foot? For my son and I's canoe trip in Atikaki Park, MB we used the same approach as @OutsideInND (aka wet-foot). I was skeptical at first, but a good lightweight hiking boot (fast-draining w.removable footbeds) and good quality synthetic socks was a great solution. We wore Merrell Moab Ventilators mid-top for ankle support (dropping your feet into ink-black water while dancing in/around bowling-ball sized rocks). They also performed very well on the portages, even when wet and carrying heavy/awkward loads on the Canadian Shield granite. No blisters or hotspots either. Just had to spend a little extra time to get them as dry as possible while in camp. Probably won't last much beyond 1 season of constant use is the main downside.