I use a boot pack as a carry on. If you are at all worried about an airline losing your luggage, skis are replaceable and rentable, a good pair of boots isn't immediately replaceable
Although if you cannot carry on, this trick seems to work for me;
There is really no good reason for airlines to give you baggage fees and most airlines are willing to forego the fee and accommodate you. If you are checking your skis– which you most likely will– check the boot bag as one. You simply explain that boots and skis go together on nearly airline as one bag. Just plead you case and make sure that THEY are the ones who seem unreasonable.
There are ton of practices of moving ski gear and that is pretty tried and true one