I would backshift to "was" in that case, but if he just said it a moment ago and I simply couldn't hear him, then "is" is okay.
Him: It's going to rain
Me: Sorry, I couldn't hear that.
Him: It's going to rain.
Me, to you: Could you hear him?
You: Yes. He said it's going to rain.
Me: Thank you. You don't have to shout.