The answer by @cavila is only part of the solution. You can put the div tag for the chart in the popup, but the issue arises then because you will need to listen to the ".openPopup()" event to then have the raphy-carts javascript execute. If you do not do it on that event, then when it executes it will not find the div tag because it has not been inserted into the DOM. It looks like leaflet supports event listening so you will need to add something like this to the code above:
map.on('popup', function(e) {
//Run the chart code here like this
var chart = new Charts.LineChart('chart1');
chart.add_line({
data: [[1, 828906, {tooltip: "my special point"}],[2, 566933],[3, 584150],[4,
1072143],[5, 1622455],[6, 2466746],[7, 2427789]]
});
chart.draw();
});