For data containing gaps or uneven sampling you must use the application LOMBSCAR, which employs the LOMB-SCARGLE algorithm, or possibly, SINFIT, which performs a least squares fit of sine waves to the data.
The document "user_006" also gives an account of the performance of a CLEAN algorithm. This is available from Harry Lehto at Southampton (username: hl@phastr.soton.ac.uk). Interested users should contact him directly.