They both need to be in the air flow to work. So, assuming the same size, there shouldn't be a measurable difference.
Now, if you are buttoning up a stock car's aerodynamics, the FMIC might be a better choice. Sitting in front of the radiator means that only one hole is needed to get cooling to both. Where as the SMIC might need its own hole. The intercooler itself isn't slicker in the airflow, but it could allow a cleaner nose and belly pan.