Yes, CanvasJS works well in flexbox layout.
CanvasJS Chart automatically sets the width and height of the chart according to container’s dimensions. When the container’s dimension is not specified it takes up the default width & height(500px X 400px). Setting 100% width for the Chart-Container will work fine in flexbox layout. Please take a look at this jsfiddle.
If this doesn’t solve the issue, kindly create a jsfiddle with the issue you are facing so that we can understand it better and help you out.