Haines or Skagway
If you cannot work out both Skagway and Haines, I would choose Haines. Haines is a great small beautiful town where cruise ships do not dock. The ride in and out of Haines to Haines Junction is tremendous (beautiful, great road, etc.). Having said that, if you are taking the ferry in order to go to Whitehorse, Dawson City, Inuvik, Dawson City, Tok, etc., you might want to go to Skagway to go straight to Whitehorse. I have been to BC, Yukon, and Alaska, 3 out of the last 4 years and Haines is one of my favorite places. That is just me.