Well, the VC was basically a spent force after Tet and the NVA had to infiltrate through Cambodia to take up old VC positions. I would assume the NVA as a result, because they would have been responsible for the vast majority of casualties after Tet.
Also, the NVA was capable of launching prolonged offensives and seizing territory, which the VC were not. Most American combat fatalities were associated with seesaw battles over territory and counterattacks. American offensives generally were a lot lower in casualties because the amount of firepower employed made the combat portion negligible, for the most part. This firepower was the reason why the North Vietnamese suffered such massive casualties in the war, as well.
There is also the fact that a good number of US fatalities in Vietnam were non-combat from accidents and friendly fire. As in most 20th century wars, the majority of combat casualties came from mortars and artillery rather than small arms fire.
The VC's area of operations where they were the strongest and probably caused the most casualties was in the Mekong Delta. Combat there was intermittent, however, and heated up in 1967 before becoming a bit less active of a sector.
Most of ARVN's casualties before 1965 were from the VC, however.