When you say "boiling it out" do yo mean putting the entire pot into a larger pot and boiling it? If so, for how long?
I put the pot in a medium sized sauce pan, around 2 quarts, cover it completly with water, and bring it to a boil over medium heat. I shut the heat and leave it until it's cool enough to handle, rinse it out, and dry it. I don't know if there are better methods, but I'm pretty sure this cleans it pretty good and kills off anything that shouldn't be there.