Welcome to FT.
I think you need to just check the various companies and see which one offers the best options. When are you planning on the rental?
I did a quick check and it looks like Juneau will be cheaper than Haines or Skagway but then you need to pay the ferry cost to get the car to Haines or Skagway. So check the options. You will pay pretty dearly for the one-way drop though,.