according to this Slate article (verified by US Bureau of Prisons) there are "139 domestic terrorists" in US prisons.

http://www.slate.com/id/2219268/

added by Jenna, based on radbiblio's research:
as of 4/25/09 -- number of people incarcerated in federal prisons for national security offense: 99 federal bureau of prisons: http://www.bop.gov/news/quick.jsp#4