"Would you accept someone of a different race as a neighbour?"
and
"How often do you see racist behaviour in your neighbourhood?"
You could also look at mobility of foreign workers of as opposed to native workers of a similar background. Unfortunately the world value survey results don't really support your case. You'd want the racism broken down by ethnicity I guess if you believe that the Japanese are particularly racist against other Asians.
The refugee figures help support the idea that Japan is more racist (Japan accept far fewer refugees than other countries), but as this is a political issue, rather than based on the reaction of individual Japanese people, it's harder to draw conclusions from this.
But yes, I don't really find a comment by an individual, or unquantified data from wikipedia very compelling.