They are both correct, but have different meanings.
The a-word construction indicates a lack of word, whereas the anti-word construction indicates something against word.
In your example, something which is "achronological" is something without a time-based order. For example, I could say my notebook is achronological, as I write on random pages on random days.
Something is "antichronological" (this is a odd word however) if it is in reverse chronological order. For example, if I wrote on my notebook from the last page to the first page, I could say it is antichronological.
chronologisch ungeordnetorin verkehrter zeitlicher Reihenfolge. Though I would not usein verkehrter chronologischer Reihenfolge. – bernd_k Jun 01 '11 at 20:14