Alaska is mainly about the itinerary, IMO. From the options listed, it looks like your choices are between Skagway or Sitka; Tracy Arm or Glacier Bay. I've been to all but Tracy Arm, so I'll address Skagway and Sitka.
Both are fantastic ports. From Skagway, you can take the White Pass & Yukon railroad for amazing views, and you might add on a trip to Carcross in Yukon Territory, as we did. Sitka was also amazing, and is filled with history. Sitka is also a tender port, but we didn't find it to be a hassle. Because of its small size, Sitka is easy to do on your own, and the savings can be used to do more extensive shore excursions in Juneau and Ketchikan. I enjoyed them both, yet I give a slight edge to Sitka as it is not on many cruise itineraries.