Remove the spare and dry that area, then sprinkle something that will show that it got wet such as baking soda, flower, or baking powder all around in the spare tire area. Then wait for it to get rained on or hit it with a water from a hose. That should show you exactly where it is coming in to that area. You will probably have to find the first entry area that is higher than that and seal that first. Test the spare tire area again without sealing the seams in the spare tire area, to be sure you stopped the first entry point.
If it's a roof seam, remove the seam sealer of the roof, dry it, put a small amount of a good epoxy in the seam line and let it dry. Then put new seam sealer on it.
If it's an external seam, it is wise to do all the external seams because if one failed, the others are likely to leak soon.
NAPA and other auto parts stores and Amazon sell seam sealer.
After you stop the first entry of water, let the vehicle dry between the walls where the water ran to the spare tire area, then after you verify water can't get in the first entry point, use water and rags to clean away all the powder, dry it and seal the seams in the spare tire area. Depending on how it looks, you might have to first remove the old seam sealer in the spare area before adding more.