My wife and I are planning a trip to Alaska in early September. We will be in the Seattle area and are considering extending our stay 10 - 14 days travel to Alaska. We are now concerned that this is the wrong period to visit. We would like to see Denali if possible and perhaps the inward passage but not by cruise ships. We are physically fit and would also like to do some day hiking. Any suggestions would be helpful.

If you're going to see the SE Passage by means other than a boat, please let us all know how you accomplished this miracle. Otherwise, you could consider using this means of travel.

A cheaper, quicker trip through the Inside Passage is by ferry from Bremerton. Google the Alaska marine highway. You can take it to Valdez, Whittier or Homer on the mainland. But with only two weeks, I'd fly to Anchorage and rent a car. Great day hikes are in Anchorage (Chugach State Park), the Kenai Peninsula and Palmer. It's the wet season, so bring rain gear. And don't plan on seeing the big mountains and you won't be disappointed. On the plus side, September is the prettiest month to visit. The leaves will be turning, the tundra redding, and the mountains getting whiter. It's my favorite month. On a clear day, blow $200 and go flightseeing over the mountains from Willow or Talkeetna. Book a flight that lands in the Don Sheldon Amphitheater on Denali. There are also flights that circle Denali and Foraker at height.

Hey #2, the OP could google for the AK Marine Highway or they could click the link I gave in #1.

As far as I'm concerned, the perfect time to visit Denali NP is late August. The tundra is showing off its autumn colors (picture the best New England autumn you've ever seen, then scale it down so that everything is less than three feet tall), and the nights are long enough to see the aurora borealis. Early September would probably be pretty comparable, though winter can start to come on very quickly at that time of year. Be prepared for snow in the interior and at higher elevations.
Two weeks isn't that much time, but if you want to do both the Inside Passage and Denali, I'd take the ferry as far as Juneau (2-3 days), then fly to Anchorage and drive to Denali. If you wanted to spend more time in the southeast, you could also take a ferry from Juneau to Glacier Bay NP, though this only runs about every other day.
Denali NP is worth spending a lot of time in, if you're at all interested in camping, hiking, or backpacking.