Great question.Setting and related elements--such as weather--can often express the mood of a work or foreshadow elements to come (see previous response). Here are a few ways to think about the question:
1) Put yourself in Fitzgerald's shoes: what is added to the story if by making it rain? What changes if it is, for example, sunny and warm?
2) How does the rainy weather here compare to other important chapters and events in the book? It is extremely hot in both chapters 2 & 7, for example. Think about how the reunion of Daisy and Jay in chapter 5 contrasts with the memory of their first kiss at the end of chapter six. How do these scenes differ?
3) Think about Nick: what is he both feeling and describing in Chapters 5 & 9? How might rainy weather reflect these emotions and descriptions?
4) Use a reader response approach and think about your own feelings about rain: what mood does it put you in? How does it change your behavior? What senses--touch? smell? etc.--does it evoke in you?
Many have written about the patterns Fitzgerald used throughout the book, so it really is all connected! Think about the use of time in this chapter, like when Gatsby stumbles into the clock: the rain has driven them into the house where they attempt to reconnect and return to their past. Is the rain, then, a symbol of the their love escaping the outside world and time, or are they trapped and unable to confront the deluge of the outside world?
Rain is most notable in chapters 5 and 9. In chapter 5, Jay and Daisy rekindle their relationship beginning with the meeting at Nick's house that Jay asked Nick to arrange. Jay is nervous, anticipating seeing Daisy again for the first time in nearly five years. Outside the rain is falling. Later, when Jay takes Daisy and Nick on a tour through his house, Daisy looks out the window and sees a pink cloud where the sun had broken through the clouds. She exclaims that she would like to put Jay on the cloud and push him around. This is the beginning of the affair they'll have leading up to Jay's death. Fittingly, it is at Jay's funeral that it is raining again. It is raining at the beginning of the relationship and at the end.