If I recall correctly, VUDU offers 3D rentals, at least they did. It's such a small market. If you have a PS3, I'm pretty sure you can rent them from Sony. I don't know if the Apple TV can pass through 3D. If I had to guess, I'd say no.
3D for me has been disappointing. So few titles and from the look of new TVs, the manufacturers are abandoning it.
What movie were you looking to pickup? Can you recommend any? The best movie we've seen (okay poor movie, but good 3D) was My Bloody Valentine 3D.