First off, I find it really odd that your LHBS doesn't sell tubing by the foot. Almost every LHBS I've ever been to sells it this way.
That being said, I would always use Food Grade siphon tubing. Even if the wort is cooled, you don't want any potential leaching or odd flavoring going on, and food grade siphon tubing won't do either.
If your LHBS won't sell it by the foot, try a hardware store. They often have similar products. You're looking for silicon, reinforced vinyl, or similar. If you can't find it at all, you can always order it online from Midwest Supplies, MoreBeer, or a number of other online brewers supply shops.