Port south, starboard north (this goes for virtually any West Coast-Alaska flight). Best chance of viewing aurora and mountains.

If you choose a starboard window seat, you'll likely just be looking down on water and will be on the wrong side of the plane for any northern lights (since you'll be looking southwest). Even if the plane takes a more inland route over the Inside Passage, the crest of the Coast Ranges (with all the majestic peaks and glaciers) is still to the east (along the Canadian border).