Try quart take-away soup containers. Whenever we get Chinese, I always get a quart of Wonton soup. It comes in this great 5 inch wide x 6 inch tall clear plastic deli container. Drill a couple of 1/4 inch holes in the sides for Phrags or semi-hydroponic or in the bottom for regular pots and your good to go.
Besides, they're much more rigid and better looking than flimsy water or juice bottles.