When I view the tomcat source code at http://grepcode.com/file/repo1.maven.org/maven2/org.apache.tomcat/tomcat-catalina/7.0.0/org/apache/catalina/connector/Request.java#Request.
The URIEncoding parameter is what you're looking for. It sets the character encoding to be used when URI decoding the query string.
URIEncoding
You use it in server.xml as an attribute of the Connector entity.
server.xml
Connector
If successfully used it in the past.