Just been with Thomson Ski and we had to put the bootbags through in the hold with the rest of luggage...good news was that we didn't have to pay any extra even though this put our combined KG over the limit!!
Balkan also make you put boots in hold. Last year we were waiting ages for them to come through at other end - boot bags were last items on belt! This year we've got ex large holdalls and intend packing boots in with rest of stuff.