I've dug up official numbers from the Department of Defense - details are below. I hope this is helpful!

A google search for "Department of Defense fiscal year 2006 budget" yielded President Bush's request for DOD funding for FY2006 here. Page 8 of the PDF breaks down discretionary funding for RDT&E (Research, Development, Test and Evaluation), which is 69.4 billion for FY06 and 66.8 billion for FY07.

To further break these numbers down by university spending, I clicked on the link at the end of the document labeled "Copies of DoD budget documents are available at the following Internet address."

This yielded the "Defense budget materials for the FY06 budget." Clicking on the section called "Research, Development, Test and Evaluation" reveals a detailed PDF file. The data is a bit complicated (sums are broken down according to Army, Navy, Air Force, etc), but line-item budgets for each department include amounts for "University Research Initiatives" and "University and Industry Research Centers." I believe that totaling these line items would provide a good estimation of the amount of money U.S. universities received from the Department of Defense for research in FY 2006.

Similar data can be found for FY 2007 here.