The United States has finished higher than Japan in most of the tournaments the two play in. The main reason Japan is rated higher is they have played in more tournament, two November World Cup age tournaments that the United States chose not to participate in. The voting system tends to favor quantity of tournaments played rather than quality.
Below are the top ten countries in baseball. You can see the complete list at WBSC.org.
1) Japan - 5598
2) United States - 5414
3) Korea - 4908
4) Taiwan - 3747