Is it better when analysing a passage to make point thematically or chronologically?

There is no right or wrong way of setting out your analysis. As long as every point has a topic sentence, a quote or reference in order to back up your statement, and an analysis of how this quote relates back to the question it will get credit.
A-Level literature exams are generally time pressured so I would personally recommend approaching a passage chronologically. This means that you do not waste valuable time trying to find good quotes and potentially losing your train of thought. It is vital, however, that you talk about elements throughout the passage. There is a risk that you will go too in-depth at the start of the passage and leave out the second half. Make sure that you have your main points down and then you can go back and add in smaller points.