Depends on the sort of boots you have and the material they are made from.
Baking soda absorbs moisture so try sprinkling a lot in to your boots and leaving it at least overnight before tipping it out. This has the advantage of neutralising sweaty smells, too.
If your boots have removable insoles, take them out and replace with new ones.
You can put some footwear in to the washing machine, if you know the make check out their website for washing instructions.