They are both correct, but have different meanings.
a-word construction indicates a lack of
word, whereas the
anti-word construction indicates something against
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.