The Hokkaido International Foundation (this program is not eligible for W&M transfer credit), International Christian University, and the Inter-University Center. We also recommend Middlebury College's Summer Language Schools in Vermont.
The University of Colorado at Boulder offers lots of information on Japanese study abroad opportunities.
Students can enroll in summer programs both in Japan and at various American Universities. Tuition is paid directly to the target institution, and credit transfer must be discussed in advance with William and Mary program directors.