Put the bottle in a smaller container of clean water inside the larger container of water with the top sticking out of the water so it doesn't overflow into it. It'll take longer to boil without the convection but you'll get there eventually. You can fashion tongs out of sticks to pull rocks back out after their heat has mostly transferred to the water while you put newly heated ones in.
That can get you sterile water, although it's extremely difficult to do and involves many more rocks than you'd imagine easily 5x the mass of rock to water to get a rolling boil for a full minute, but it doesn't get you clean water. Now you have sterile water with a lot of potentially very unpleasant dissolved solids. Certainly not something you'll be using to feed an infant.