The issue with boiling water is that it's not necessarily going to be boiling hot when it reaches into the Therminator nooks. If you happen to have a pump the best best is to recirculate your boiling water through it a few minutes, from both sides. "In the out" and "In the In".
Also - this can't be emphasized enough.. you need to clean it immediately when you are done with it. After you have gotten your cool wort taken care of the therminator should be the first thing on your list. Be sure to start by running "in through the out" first, then back again. Also, don't allow and hops to get in it.
I had been thinking that sterilizing in an oven would be a pretty good way of making sure everything is clean. 170 degrees for 1 hour.