I got smoothie stains on my Vitamix that were probably complicated by hard water. I tried vinegar, that helped a little, I tried clorox, that didn't have any effect. After googling "removing stains from vitamix" I found a site- Everyday Tastiness that had the following solution:
Pour 1 cup vinegar in container, add 1/4 c baking soda. It will bubble up, let sit until bubbling subsides. Then add 2 cups water (I used warm) and let run on high for 5-7 minutes. I then let that sit for 2 hours. Rinse, and if any stains remain, I used a soft bottle brush and they were easily removed. I then filled the container with water, and a couple of drops of detergent and cleaned and rinsed as normal.