In Juneau there as several bus companies that will shuttle you to the Hubbard Glacier visitor's center parking lot and you can explore on your own.
Skagway, the train up to the pass is interesting, but you can also hike a trail in that direction and turn back when ready.
Ketchikan on our first Alaska cruise we did the totem pole visits, Saxman Village, etc. Next time we went salmon fishing on a private charter and loved it. Caught as much as we wanted to pay for the processing and shipping home. Was great salmon, but on a per pound basis it was very expensive. Nonetheless, we'd do it again.

boom_boom is righht on the money. It's tougher with the 2 year old.
Juneau Sky Tram would be inexpensive. Walk around town is good. Whale watching or misty fjord is "must seee" for Ketchikan but I am not sure the 2 year old would enjoy that, plus it's not cheap. There is a nice garden at Skagway that the 2 year old will enjoy.

Okay so for Juneau - possibly plan on the bus that will shuttle us up to the Hubbard Glacier. Is this bus something that we won't miss seeing and it's clearly marked that it goes there or will we need to know where to go to find it? Is the Tram something right there when we get off the ship? That would take us to the glacier as well? Or is that taking us to a different location? Which would be the better option with the 2 year old? Or do we have time for both?

Ketchikan: Saxman Village/Totem Pole visits....is this right there where we get off the ship? Is the ship's port right in town or will we need to take a taxi, etc.? Whale watching would be great! About how long would that trip last? She's a very easygoing and laid back little girl - but she does have her limitations! Can you recommend a company to consider this with?

Skagway: I did see the train (White Pass Train?) and noticed that it's a 3 hour roundtrip tour. Is it cramped or tight? Or would there be room for my daughter to walk around? Room for a stroller? Or if we did this - should we plan on the backpack carrier for her?

Sorry for so many questions. Thanks for your help!

It is NOT Hubbard Glacier it is Mendenhall. The bus loads at the dock, there are booths set up selling the tickets. The Mt Robert's tram is clearly viewable and on the dock. Don't bother if you can not see the top.

The White Pass RR, is not loaded with space, and you would be expected to stay in your seating area. It certainly is not a place to haul around a big stroller, or allow your toddler to be running around, up/down the aisles. IF you are just taking the round trip train, do realize you do not get off the train.

An alternative, would be to rent a car, IF you all have proper ID to get into Canada? Avis is the only major car rental.

Saxman Village is available via tours right from the dock.

As for whale watching, a toddler is not going to get anything out of it. It is not like Sea World. It requires the ability to follow and track. A toddler is not capable of this, sorry. It is 3 hours in a confined space with no way out.

This age's behavior can not be predicted, and doesn't matter if "easy going". As only a GENERAL comment, sometimes parent's perceptions aren't reality based. With the high cost of tours, no one wants their's ruined by a melt down child. Again, only general comments, that should be a consideration.

Walking tours are available in each port. Head to your library and take out Fodor's Alaska, read up on the areas. The more you know, the better your choices will be for your touring priority.

Juneau: We liked the Mendenhall Glacier, Stae of Alaska Museum, Icy Straits glacier tour, State capitol. We didn't get a chance to tke the Mt. Roberts tram and go hiking.

Skagway: Loved the White Pass & Yukon RR, and people certainly did walk around during the trip. Also liked the Klondike Gold Rush National Historical Park exhibits & film, walking tour, City Hall Museum, Corrington Museum.

Ketchikan: Liked Totem Bight State Park, the SE Alaska Discovery Center, Deer Mountain Tribal Hatchery and Eagle Center, Totem Heritage Center

This is what we did last summer:

Victoria taxi to Butchart Gardens
Juneau taxi to Mendenhall Glacier, fish hatchery, museum
Ketchikan. Hired Ketchikan Cab to take us on a tour. Book ahead.
Skagway rent car at AVIS drive to Yukon Territory Carcross.

Victoria and Juneau ---hire any cab.
Ketchikan and Skagway must be reserved ahead of time.

In June we're going on our 3rd Alaskan cruise and have chosen not to book any ship excursions because of the improbable weather....June is likely to be overcast, sprinkly, so hiring a taxi or going on city transportation will allow you to decide at the last minute whether it is a good day to do whatever you had planned.

Note from the above responses - there is virtually nothing "right there" in any of these ports other than jewelry and t-shirt shops. Anything of interest involves additional transportation once you get off the ship. You can most easily walk "downtown" in Skagway, but it is a town primarily owned by and designed for cruise ships (did you know that the cruiselines own most of the businesses?) If you have been on warm water cruises, ports are very different - the real Alaska involves tax, car rental, bus, train, plane.

So redefine "on your own" - there is not much to be seen with just a map and a pair of shoes.