National Science Foundation, Division of Science Resources Statistics, Academic Research and Development Expenditures: Fiscal Year 2004, NSF 06-323 provides a view of R&D spending at universities in the USA.

Spending over the last 5 years in billions: $30.7 in 2000; 32.8; 36.4; 40.1 and $42.9 in 2004. For 2004 the funding source for the spending was:

Federal Government: $27.4
State and Local: 2.8
Industry: 2.1
Institutional: 7.8
All other: 2.8

Also for 2004 of the total $32.3 billion was for basic research and $10.6 billion for applied research and development.

The schools spending the largest amounts on R&D in 2004 and the spending in millions:

Johns Hopkins $1,375
UCLA 773
Univ of Michigan (all) 769
UW - Madison 764
UC - San Francisco 728
Univ Washington 714
UC - San Diego 709
Stanford 671

The publication includes a huge amount of data on current spending and historical spending.