We went last cruise of the season in 2014. I think the major plus late season is that you are less likely to be unable to reach the glacier on scenic sailing day; that seems to happen more early in the season. Weather wise, I don't think there's any way to predict. We had mostly 60s with just one drizzly day. I did an Alaska cruise in the late 90s where we were first cruise of the season (early May on HAL) and it was so hot several days that I wished I had packed shorts.
We were able to spot wildlife on both trips, though the early September trip was at the end of the salmon run so we saw fewer salmon.
(Does anyone else care about salmon spotting, or is that just my son?) I would personally go on the cruise if I were you, OP.
DCL to Alaska is my second favorite vacation of all time (having been displaced this year by our trip to Costa Rica).