I don't think anyone is trying to cover up the Oil for Food scandal on behalf of the US. If we were, we would never have exposed the scandal in the first place, but simply used it as blackmail for UN cooperation in Iraq.
From what I've seen, Negroponte is one of the good guys -- but it's getting harder and harder to tell.
In this linked article, he is criticized by the left for supervising the creation of the El Aguacate air base in Honduras. The air base was used for US training of Nicaraguan Contras back in the '80's.
We didn't expose it.