Have heard that t tree is good for getting rid of mould in the home, but never tried it myself, so not sure if it would work on the boots. You could test patch a bit on the inside to find out. If it works let me know.
Ooh we have some tea tree oil! will give that a go! If not ill get hold of some virkon (bet the smell takes me back to work experience at the vets! can remember loving it!)