Just like you work any other tile - with the Citizen Management controls from the city that you wish to work Krakatoa from. Mind you that no tile may be more than 3 tiles from the city you intend to work it in. As long as it's within that range, go to the city screen -> Citizen Management -> Manual -> click on the tile to select it.
You don't need work boats or workers because Krakatoa is not a resource, it's a terrain feature. Two different things - and in fact, unless you're running a DLL mod, since all natural wonders qualify as mountains in that they're impassable, you shouldn't be able to get either unit on Krakatoa to improve it.