There are 15 Executive Departments whose leaders are secretaries appointed by the President and approved by the Senate. These secretaries constitute the cabinet. Bureaus and agencies are subdivisions within departments. There are various kinds of bureaus and agencies: independent regulatory commissions, government corporations and independent research agencies.
Independent regulatory commissions are agencies of the executive branch of government that controls or directs some aspect of the economy. They are intended to operate somewhat independently of the White House. Independent regulatory commissions include OSHA.
Government corporations operate in a market setting and perform an essential economic activity not feasible in the private sector. For example, USPS would not survive without government funds; similarly, AMTRAK was socialized because it was deemed too crucial to let collapse.
Independent executive agencies include the Smithsonian and CIA, and function somewhat independently of the White House. However, the President can directly affect policy by appointment power and executive orders. For example, President Bush issued an executive order to stop funding of NSF's new stem cell research.