We did the Juneau tour. They are both pretty much the same so I'd go for price. They use wheeled carts that hold six passengers and the musher. You'll be amazed at the power when the sled takes off (almost literally).
The Juneau camp is a training site for Iditerod teams, and I suspect the Skagway site is the same. They train the dogs in the panhandle during the spring and summer because it is cooler than it is farther north (really). The dogs are most comfortable when it is below zero! These are Alaskan Huskies which is a distinct mix of breeds bred to various traits. The tours help pay the team costs and also help train the dogs to get used to strangers (during the Iditerod volunteers help the dog teams at break areas).