My cruise I'm referring to was mid to third week of September.
Keeping in mind that predicting weather isn't necessarily that accurate...
There's a pretty good likelihood that it will be rainy and chilly (sorry). I love cold weather, but yes, it was cold. We couldn't get into College Fjord because of the rain, low clouds and ice floes. We docked IN Anchorage (most ships dock in Seward or Whittier - a several hour trip into Anchorage). The Kenai Peninsula, IMO, is fascinating. I thoroughly enjoyed visiting the Alaska Wildlife Conservation Center near Anchorage (and, yes, it was cold/cloudy/rainy/snowflurries). I absolutely loved the Alyeska Resort in Girdwood, near Anchorage. Both are on the Kenai Peninsula.
I found it fascinating to learn that Captain Cook, famous for his Hawai'i/South Pacific explorations also found his way to Alaska - Cook Inlet/Turnagain Arm...
Turnagain Arm of Cook Inlet; Anchorage to Girdwood
To view the Northern Lights, you need a dark, clear sky. I've yet to see them in Alaska (I've seen them elsewhere). Very unlikely you'll view them in Glacier Bay because you cruise there during daylight hours. Your best bet will be the farther north you travel - but again, there are no assurances.
Hope this information helps. Enjoy your cruise!