The two glaciers we went to at the different ports were so different from one another. I'm not certain if all tour operators at each port go to the same glaciers but here's what we visited and saw from each port.
From Skagway, we used Temsco which took us to Meade Glacier. The operator was great. We booked through disney because we were able to book for our three year old boys through disney even though I think they did not meet the age requirement when attempting to book directly through Temsco. Temsco was great. There was a big shuttle bus that picked us up directly from the port and brought us to their facilities where they provided secure lockers for our belongings and out fitted us with glacier boots to go over our shoes. The weather was wet so they also had rain gear for us once we arrived at Meade Glacier. This Glacier was how I had imagined a glacier to be, blue and icy with large crevasses and flowing rivers of water through the icy fields. The footing was a bit slippery in some spots and we had to be cautious around the larger crevasses, especially with our two boys and our daughter. We spent about 20-30 mins touring the glacier. We were welcome to tour independently so long as we did not venture too far from the guides or to follow the guides and ask questions as they came up.
In Juneau, we used ERA and flew to Norris Glacier. This operator was also great. Again, we booked through disney as the three year olds were accepted. We spoke with two families on the excursion with us who were disappointed that they left their 3-4 year old children in the kids club thinking that they did not meet the age criteria for this excursion. ERA picked us all up in a large bus directly from the ship and brought us to their facilities. They too provided glacier boots. Unlike Temsco, ERA did not have boots small enough for our 7 year old daughter or 3 year old boys. They just wore their sneakers and it was a non-issue. We flew to a dog sled camp which was located on a part of the glacier which was snowy rather than icy. I would not have known we were on a glacier had we not flown over the icy fields leading to the camp. The weather was great so no rain slickers were provided so I can't comment on whether or not they would have been available. The dog sledding was great, all members of our family enjoyed this excursion the most of all our activities on the cruise.
If we had to choose one to do over, I'd have to say we all would choose the dog sledding. This would be due to a combination of factors: our kids love dogs, weather was great, saw the icy glacier from the air and got to play in the snowy part of the glacier (we as parents were not always on edge that one of our kids would fall down a crevasse).
I hope this helps you decide on your excursion based on what you were hoping to see on the glacier. If you plan on doing only one excursion to a glacier, I'd look into one of the combo tours. I remember reading about longer excursions which provide a walking tour on the glacier followed by a dog sledding experience. I hope someone can confirm but I'd assume the touring portion would occur on an icy glacier then the dog sledding would occur on a snow covered portion of the glacier. This would give you the best of both worlds. Also, if I had to choose one port to pick this excursion from, I'd consider skagway as this port town is very small and a long excursion may not necessarily preclude you from touring the city before or after your excursion. Juneau is much larger and has other things you could do if not opting for an excursion (i.e bus to mendenhal, mount roberts tram, city tour, tracy's crab shack). A long excursion in Juneau may limit your ability to fully tour this city.