My 2 year old son has been throwing up and it smells like feces really bad. Should I take him to the hospital ?

Yes. A child that small can become dehydrated quickly and given you don't know the cause, better to be safe.

I meant to tell you that fecal vomiting can be caused by small bowel obstruction, which can certainly be an emergency. Go now... Don't wait around for it to resolve on it's own.