What type of work, what type of hunting, fishing, shooting, what will your budget be, are you bringing a family? youre talking apples and oranges with these two places.
Both places an ocean boat or knowing someone with one are the keys to enjoying those places for what they are. Homer is on the road system even if it is the dead end of it, little easier to get certain things since you can drive it in from Anchorage, Homer is a bit warmer than most of south-central during the winter and a little less snow, if you have a boat, there's some good blacktail, black bear and goat hunting in the area. Brown bear can be had but if youre only here for two years you'll barely qualify for residency for goat, sheep and brown bear. Non-resident tags and license are expensive so be prepared to pay those fees and not be allowed to hunt certain locations, animals because of it. Homer is a quirky, artsy kinda liberal fishing town summer time its booming, winter it gets very darn quiet which is the same with Juneau.
Homer you can drive to some decent fishing freshwater Kenai or Anchor, deep creek for all five salmon species, trout, dollies, steelhead in the fall. You may be able to draw a peninsula moose tag but not knowing the area or anyone thats a resident, unlikely you'll get anyone to give up their hunting spot. Most alaskans would rather give up their firstborn than their moose spot. Fred Meyer, Walmart etc... for other necessities outside of the grocery store are about a two hour drive to Soldotna although there are some super cool little local shops.
Juneau has a climate more in line with Seattle and is temperate rain forest, not much in the way of a road system as its on the Alaska marine highway, only way in is plane or boat, ferry has had a ton of budget and maintenance issues over the last few years and in the winter does not run with nearly the consistency. The take off and approach into Juneau can be a bit scary if you don't know what youre getting into, very steep climb out due to a mountain at the end of the runway. Lots of rain, its a main cruise ship destination during the summer and a lot of the city shuts down for winter much like homer. Great black tail and black bear hunting on the surrounding islands. I believe I saw an EO from ADF&G this year that sheep and goat were shut down in the area this season due to low numbers. You won't have much opportunity for moose out of here and no caribou. Youre closer to Seattle here than the rest of Alaska. At least with homer you can drive up north and get into some other hunting areas and experience the rest of Alaska. I love both places but they are very different and also similar.