I just re-read your post and noticed that your friend is covering the expenses for your trip. If that's the case, go to Skagway. There's much better and a much wider variety of accommodations there plus its a longer ferry ride. If its his dime, make a great trip of it. Haines is a nice place and has places to stay and places to eat but they are no where near as many or as good as what's over in Skagway. The locals here tolerate tourists and travelers but I wouldn't go as far as to say that we even come close to catering to them. If its your dime though, you'll spend less money in Haines (there's very little to spend it on over here in comparison). Skagway will be busier during the day but they usually prod the tour boat cattle back onto the boats close to dinner time. They won't come back again until morning. Both routes are incredibly beautiful and the good news here is that you really can't go wrong with whichever you decide.
My other bike is a kayak.