Alaska in September

...after three trips there to all five major islands there is nothing new to see...

Well, that's probably a bit of an overstatement - I've been to Hawaii more than a few times and I wouldn't say I've seen/done everything there. But on to your question...

I've spent a fair bit of time in Southeast Alaska (where the cruises go) into October. The worst of the summer tourist crowds will have abated by mid-September.

Weather-wise, it's a roll of the dice. In Southeast Alaska, late September/early October could be quite pleasant, with good amounts of sunshine and clear skies during the day, nights will be cool, maybe a lot colder than you might expect (no snow, but decidedly chilly). On the other hand, it could be rainy, cloudy, drizzly, misty, foggy, with low clouds and lots of moisture. It's a pretty safe bet that you will get at least some of that (maybe a lot of it), so you will need to plan accordingly.

Climate change might work to your advantage here in some ways - our early fall weather has tended to be warmer and dryer than usual in recent years. OTOH towards the end of summer, wildfires from the US to Siberia have turned our air into a brownish-gray soup, obscuring views and making breathing a chore. There's no way to tell exactly what mix you would experience, but I would suggest you be ready for at least some of each of these phenomena.

My only visit to Alaska was in September. I think I arrived in Anchorage about Sept 17. It was warm enough to eat lunch on the restaurant patio (high 60'sF), but went to Denali about 5 days later and it was the last weekend opened for the season and overnight temps were freezing. I guess that puts my cruise dates similar to yours. Polar fleece and rain coat. I enjoyed all my activities, though the small plane flight over the glaciers in Juneau was cancelled after my early morning flight of the day - due to foggy conditions. It was also the last cruise for Princess for the season. The Coral Princess was well designed with a covered swimming pool at the back ( I often had it to myself), and they had a large atrium area for nature viewing in cooler weather. We didn't have a balcony, but it could be lovely with a deck blanket and a warm beverage. Speed is slow moving through the Inner Passage.
I quite enjoyed the timing...but I grew up on the BC west coast, so nothing new for me.
It was definitely a more geriatric crowd onboard, but there were a mix of ages. Mostly American, but some internationals. The down side is that at the time, hand wash stations were non-existent and no purell stations at elevators or restaurants. I came home with H1N1 and pneumonia. Take your hand sanitizer and avoid the buffets.

While the only cruise I've done up that way was earlier in the year, we work the Alaska ports fairly often. Depending on where you're going September is usually the tail end of the "good" weather. This means you can still have shirtsleeve days, light jacket days, and rain jacket days. The further south you are the more likely the weather will be warmer, although the rain can be very much a local concern. Plan for rain, don't let that bother you. Folks in the PNW are used to doing pretty much everything in the rain. The chances of snow are minimal. It can happen, but usually it doesn't get down to sea level until later in October.

Ketchikan and Juneau are easy to walk around. Skagway is really small, but if you do go there take the train up to the pass; the scenery is incredible. Days are getting shorter then, so expect that. Anchorage is a big city (for Alaska), but if you're there any length of time try to get a car and take a ride out of town along Turnagain Arm.

A rain jacket/light parka is a must; you may not need it, but if you do you'll want to have it handy. Take a hat, umbrellas are for tourists. Sweaters and fleece are a good idea. Make sure you have waterproof shoes or boots. If you want photos take a good camera with zoom. You'll see all kinds of wildlife.

One thing I noticed on the cruise I took, most folks sleep late. I don't, and walking the deck at 6am I saw whales and orca that 95% of the people on board missed.

I should recommend, that if at all possible, do a one way cruise, not a return to same port.

Tourist season pretty much closes down on Sept 15th as mentioned previously.

However, sometimes the weather is nice through Sept. albeit cooler.

Cruise Critic has a "Find a Cruise" feature you can use to see what's available on what dates. September is late in the Alaska cruising season so I don't know what you'll find, but give it a try. As others advised, expect some rain and chilly mornings/evenings.

I'm not sure why another poster advised against a round-trip cruise. Repositioning cruises between points A and B can be fun and cheaper, but you have to get back to wherever you started. The only port that's repeated is where you start and finish.

To clarify my post. One way Alaska is not repositioning. It is a common option in Alaska to do Vancouver to Whittier one week, then Whittier to Vancouver the next all summer. I prefer the calm and scenic route doen the Inner Passage (betweeen mainland BC and Vancouver Island). A return to a US port takes you to the west of Vancouver Island and rougher seas. Is the cruise is just for cruising sake and not about scenery, then it matters less. And is a moot point in this case as they don't seem to be offered that late in September. There are a few other options, including a Sept 22 sailing.

We did an Alaska cruise in September of 2016 from Vancouver to Seward. After the cruise, we spent four days going to Denali National Park. Denali is a must see in my opinion.
Our cruise was for a week in the first week of September, ending in the second week. The hotel in Denali were we stayed closed down for the season the day we departed to go back to Anchorage for our flight home. That was around the middle of September.

Not sure when the daily Tundra tour at Denali ends, but I think it ended a couple of days after we departed. I suspect by 9/22 that Denali will not be a viable option.

The latest time for me to cruise to Alaska was the first week in September. There were still plenty of whales. We left Juneau after dark and saw the Northern Lights from the ship, until the moon rose; we had to go to a balcony as the deck was too well lit. September is often an extended summer-like weather, but without the fog. The salmon should be running and the humpback whales will still be in the Alaskan waters. September is when the t-shirts and souvenirs are on close out. Skagway will almost be shut down, as few people live there and the seasonal help will have moved on.

I'm leaving on an Alaskan cruise on Thursday. Weather already looks much more promising than here in SoCal and I'm really going to appreciate that rain!