Provided that your toy is 100% silicone, the bottom of the pot is covered by the liquid, the pot has a thick enough base to not have any major hot spots, and your liquid boils at under 450F you'll be fine. Silicone is good to about 500F (leaving some "flex degrees" in there).
Silicone is great because it is inert - water won't bother it, and even if something starts growing on it you can wash and sanitize and it will be back to clean in no time.
If the toy is true 100% silicone, it is safe to keep it in boiling water for longer periods of time, as long as there's plenty of water to keep the toy 'afloat'. One time I sterlized a silicone plug by submerging it in the bottom of a pot of boiling water with a wooden spoon, and the part that was in contact with the pot's bottom melted a little; either that cheapie so-called silicone plug was not 100% silicone, or maybe the extreme high temperature was just too much for the silicone.