What is the best time to go Early June or Sept 2?

What is the best time to take a 7 day HA cruise from Seattle? Is early June warmer than early Sept? Any other differences other than temperature?

Weather can vary greatly, but September will generally be cooler and rainier than June. I have been in late May and early a September and enjoyed May more. We only had one day of rain in May and there was still plenty of snow in the mountains. Temperatures in May were 40s - 60s. Early September was 60s - 80s, but probably above normal.

One thing to consider is what excursions you are interested in and are you doing a land tour to Denali before or after your cruise (although out of Seattle will probably be a r/t itinerary). The dates you list are a little early or late for peak times for the salmon run and bears, if that is important to you. If going to Denali, check the opening / closing times for some of the roads and tours.

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you'll have more daylight in June than in September

One thing to consider is what excursions you are interested in and are you doing a land tour to Denali before or after your cruise (although out of Seattle will probably be a r/t itinerary).

For the OP, I'd personally pick September as the weather in the Seattle area will be reliably nicer. In SE Alaska it's always a crapshoot. But what I'd actually do is a round trip out of Vancouver instead, for calmer and more scenic sailing (inside Vancouver Island on protected waters, not outside on open ocean.)

Animal sightings could be better/worse depending on when you visit. In September, you may see more bears but the salmon will be mostly done spawning (that was our experience). I think the highest number of whales is mid-summer, though we've seen some in September (haven't been in May, only March - didn't see whales during the March visit;))

Good shopping deals in all ports. End of cruise season.

What is the best time to take a 7 day HA cruise from Seattle? Is early June warmer than early Sept? Any other differences other than temperature?

We’ve been in late May and early June and the trips were different weather wise just by chance. Luck was with us on the May trip with a bunch of sunny days in the southeast Alaska portion... including Glacier Bay. We just returned from our early June trip that had a lot of rain predicted but again we were lucky in that we ended up with a lot of cloudy days with an occasional sprinkle (except for Ketchikan). Late May seemed too early for any good bear sightings. It’s well before the salmon runs. The humpbacks are just arriving from Hawaii. However, if your cruise is going to some of the smaller BC towns as well like Prince Rupert, June is an excellent time to see grizzlys on a tour to Khutzeymateen Bear Preserve. The bears come down to the shore of the river to eat the grass high in protein. They do that until the salmon start to run.

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I vote for June. I like dry port weather.

Have a look at this climate chart for Ketchikan.... September rainfall is DOUBLE compared to June. https://www.usclimatedata.com/climate/ketchikan/alaska/united-states/usak0125

Most noticeable to me is the hours of daylight. In most cases, it will be when cruising but as an example, when we sailed in August, we arrived in the dark and left Skagway at 8PM and it was already getting dark, we didn't see any of Lynn Canal. When we sailed in June, it was light until almost midnight so the potential to see a lot more. Of course, these are also times when you might be in shows or eating, etc. so whether that matters to you or not is really up to you.

May and June are historically dryer. Every month after increases the chance of rain with September having more rain compared to May and June.

I vote for dryness! I have been in Alaska when it poured the entire cruise and it was miserable.

Of course, weather in Alaska is unpredictable - all you can do is look at records. There is also more sunlight in June.