Now, I don't take the film Apocalypto to be historically accurate by any means, but I feel it is a reasonably releastic look into the way of life of Amerindians pre-colonisation. It is clear these people are not as intelligent as Europeans, they were far, far less developed and absolute savages compared to Europeans.
Now, the average IQ of a European/Amerinidan mixed country is about 90. Considering this, I would wager a guess that the optimium average IQ of a pure Amerindian is about 80, and considering the conditions of pre-colonial Americas, I would suspect the average IQ in these times was 70-75.
Very occasionally uncontacted tribes of Amerindians are found, and they have IQs that are around this mark. It was once attempted to teach a certain tribe to count (as there was no concept of counting in their language/mindset), with no success at all.
I think it is painfully obvious that there is a racial difference in IQ, there are too many coincidences for there not to be.