Ecoterrorism Prevention Act of 2004

Ecoterrorism Prevention Act of 2004 - Amends the Federal criminal code to prohibit plant enterprise terrorism (offenses to disrupt or damage a plant enterprise). Enhances penalties for animal enterprise terrorism and establishes penalties for plant enterprise terrorism. Prohibits the use of explosives or arson against animal or plant enterprises. Authorizes restitution for economic damage resulting from the violation.

Makes animal and plant enterprise terrorism predicate offenses under the Racketeer Influenced and Corrupt Organizations Act. Includes within prohibitions under the Hobbs Act denying another the right to exercise control over another's property by threatening to violate animal and plant enterprise terrorism prohibitions.

Requires the Director of the Federal Bureau of Investigation to establish and maintain a national clearinghouse for information on incidents of crime and terrorism committed or directed against: (1) any animal or plant enterprise; (2) any commercial activity because of the perceived impact or effect of such commercial activity on the environment; or (3) any person because of such person's perceived connection with or support of any such enterprise or activity. Requires the Director to report annually on domestic terrorist organizations.

Requires the Director of the National Science Foundation to make security upgrade and technical assistance grants on a competitive basis to colleges and universities.

Includes animal and plant enterprise terrorism within the scope of provisions regarding harboring or concealing terrorists and providing material support to terrorists.

Establishes procedures for designation by the Attorney General of domestic terrorist organizations. Amends the Internal Revenue Code to provide for the suspension of the tax-exempt status of such organizations.