Iris does make some of their boxes in a fairly clear plastic. However, it's not clear to me what sizes are available in this plastic.
Iris' other boxes are already more clear than most rubbermaid or sterilite boxes, but not dramatically so.
Check with Reptiletubs.com for info on which Iris boxes are clear.
For more $$ one could use Cambro's perfectly clear polycarbonate boxes. These are excellent boxes and average a bit bigger than similar sized rubbermaids. Rubbermaid makes an identical polycarbonate box but the corners are frosted. Find the Cambros if you decide to try this. They are much better due to the lack of frosted corners.
The polycarbonate boxes are fairly expensive but are virtually unbreakable. Polycarbonate had decent scratch resistance but, conversely, is not easy to polish if you do scratch or cloud the sides. Regardless, if you're careful you won't have any trouble with scratching. Don't stack the boxes inside of each other, only use soft materials to clean them, and don't leave them in dilute bleach for extended periods and you'll have a nice box for years.
Lastly, you could use whatever box you like, even solid colored ones, and route out a section of the side or front and attach a clear piece of acrylic. This would probably be your cheapest option if you can't find a clear Iris box to your liking.