How scary! Have you told your vet about it? I read that Metronidazole (Flagyl) is considered very safe, and is used to treat it. “Metronidazole has two interesting properties--the action is largely confined to the gut and it
also seems to stimulate the local immune system. Metronidazole kills off the giardia and reduces the numbers to the level the dog's immune system can handle."
Giardiasis: Diagnosis, Treatment, and Prevention The link also informs of a vacine. I hope your little guy doesn't get this.