When wood or rocks are too large to fit into a pot to boil, I have placed them in a large waterproof container (bathtub has substituted before) and soaked them for days (or more, if needed) in a high concentration of ammonia. These items are then thoroughly rinsed and ONLY placed into a tank with no fish or critters until it has cycled or the existing bacteria has removed any remnant of the ammonia. Make sure you use clear ammonia, btw!
Another method I've heard of is to use chlorine bleach to soak it, then just rinse thoroughly and then add declorinator until all gone. Seems to make sense to me!
If you can fit it into a pot, definately boil if you get the chance.