Are there still Flood on Earth at the end of Halo 3?

No. The Elites were able to stop the Flood infestation by glassing much of Kenya and surrounding African countries, much to Lord Hood's displeasure. They did this before the flood had time to spread and infect earth.

I would doubt it at the end, everyone is saluting troops who died in the war so I doubt that fighting continued. But, there's always that small possibility that that SINGLE spore is somewhere in the middle of nowhere ready to infect.