Firstly, welcome to Prince Edward Island! The autumn is a lovely time to visit the Island.
Late September can be a bit early to see a profusion of fall colours. While you may see the odd tree with its leaves having turned colour, the most prolific colours will not likely appear much before the Canadian Thanksgiving (October 9th). I do a lot of photography and, as a general rule, count on the period from around October 10-21 as the most opportune time to capture the stunning reds, golds, and oranges of the Island’s fall foliage.
That said, the Island is still lovely and green and, since you’ve indicated you will be visiting Green Gables House in Cavendish on the Island’s north shore, I think you will find the drive through rural PEI to be very picturesque.
In terms of attractions to see in and around Charlottetown, I would suggest a city bus tour or a horse and carriage ride. The city is not big and either type of tour will point out the main attractions.
If you are in Charlottetown in the afternoon and choose not to do a tour, I recommend the matinée performance of “Anne and Gilbert – The Musical” which plays at the Guild Theatre on Queen Street at 1:00pm on September 27th . This is within walking distance to the cruise terminal. This musical is high energy live theatre with lively, toe-tapping music.
I hope you enjoy your cruise and your visit to PEI!