Makes no difference, the glacier dog sledding tours are similar. With Skagway you do have a slightly less chance of cancelation, but no way to predict, as these are the most canceled of Alaska tours. ALWAYS have back up plans.
Do realize, you are two sleds hooked together, 2 riders in the basket, 1 on the "breaks", you do not drive your own sled, nor is there much reality with the breaks, your sled will stop anyway.
We did dog sledding in Juneau and LOVED it. Our ship did not stop in Skagway, so I'm not sure what else there is to do there...but I thought Juneau itself was very disappointing, there was little to do besides stroll past all of the cheesy tourist shops. So, I would suggest if you don't decide to do the tour in Juneau find another tour to take while you're there.