For carry on boots, I prefer the Transpack Sidekick Pro. It is backpack that carries your boots (as compared to a bootbag you wear on your back) so it is very comfortable walking through airports. The shape of the back fits very well in overhead compartments and holds a tremendous amount of gear and has a padded compartment for a laptop too.
The downside of the bag is that it does not protect the boots from the elements.
Interesting choice as the boots at not enclosed. I have looked at a bunch online, but all had closable boot compartments. All I am looking for is a way to transport them while flying. BTW, an iPad compartment is a requirement.