Short version is that I'm wanting to chase moose. Will be based in and around a river but may hike up and down smaller channels for several miles (with pack rafts). I don't think waterproof boots and gaiters will be enough but I have reservations about doing any serious hiking wearing waders. Not sure my feet would last in boot foot waders. Do the stocking foot type hold up to strenuous hikes? I've never tried but it seems like the folds inside a boot would wear hot spots. I can't afford to trash my feet 2 weeks into the back country. Wondered if any of the fisherman could opine, or anyone else that has had similar experience...?

Use good footie waders, wool socks, and a pair of lace up boots that fit with all that on. Sure they'll get nasty, but can be cleaned.

I ran into this a few years ago on Alaska caribou hunt/float trip on the boggy tundra. I bought a pair of these.
http://chotaoutdoorgear.com/shop/hippies/original-hippies/

You limiting factor will be the comfort of your boots and how easy your feet blister, but I had no problem hiking a few miles a day in mine for a week and they are very light. Definitely try out your boot/wader combo though before you go. I chose a solid pair of lug sole cabelas wading boots and had no real problems, but you could also get by with using these with hiking boots a couple sizes bigger than normal.

Other options include changing into and out of waders at every crossing but if the terrain is really boggy with frequent water that isn't a great option.

Another, is to just using a good lightweight pair of chest waders. If you are staying within a short distance of the water this isn't a terrible option, as you will want to wear these while in the raft anyway. Plus some water will inevitably be over your hips.

Another is to simply have good wool socks, with good boots, pants and gaiters that dry quickly and a change of clothes and just wade when needed. If you are hunting in even moderately cold weather I wouldn't go that route.

Another is to use knee high waterproof boots. But you obviously are limited in water height and they don't dry quick once they fill up.

If you are gaining elevation or hiking a ton, there aren't any great options in my opinion. Plus like any waders the "hippies" I posted aren't made for busting heavy brush so be cognizant of wearing holes in them in thick brush.

Honestly depending on the terrain and distance I might go with a completely different option. You probably will have chest waders and hiking boots with you regardless, so I would pick up a light pair of "hippies" and have your gaiters and see what makes the most sense once you get there.

Kudos. This sounds really hard to me.

Good suggestions so far. Biggest problem is I have no experience in Alaska. Guess I'll know better for my 2nd trip. Any suggestions for brands of waders to try out. I've got some cheap Hodgeman's but they make you sweat like crazy and hold moisture in.

Any reputable lightweight breathables will work (hodgemans, Cabela's, chota, etc). I would not go with neoprene or the heavier ones and i would definitely go with stocking-foot over boots attached.

Just know they aren't designed for busting a ton of brush or working near a fire and try to take care of them the best you can. I would almost consider it a one time use item and not go crazy on price if you hunt hard in them. Expect a hole or two if you hunt hard in them for a week and bring a patch kit or duck tape.

I would probably go with a pair of Cabela's breathables as they might take them back if you tear a hole in them

Again, there is no perfect solution for the terrain up there. But hunting in waders/hippies beats the hell out of wet, cold, feet.

Also, I know you are bringing pack rafts, but realistically you aren't going to be able to get very far off a water body and expect to haul out a moose.
So I don't think you will hike anywhere near as far as you think. It's nothing like you a western elk hunt, in my experience. Plus the terrain up there is so tough, it's hard to go miles in that boggy stuff that moose like. It's hard to walk in, but you aren't covering miles and miles.

I think you are right on. I'm used to covering lots of miles chasing elk, but this is a different situation. I talked to a guy that knocked a moose down last year just over a mile from the river. He said it took him 3 full days to get it packed out. That's hard for me to wrap my mind around.