The most efficient ICEs today are very, very large engines, such as
this 25000 liter two-stroke turbo diesel ship engine with ~50% thermal efficiency. I would guess that large, stationary diesel generators are also efficient, since weight isn't much of a concern and they can add waste heat recovery systems, etc.
Or if by "cleanest", you mean you'd survive the longest while locked in a garage with one running, I'd go for the Honda 1.0L 3cyl that came in the Insight with CVT. I don't know of a car with lower NOx, CO, and HC emissions.