How could be the best way of implementing a 3D fft chart?

You can use column series in Highcharts with added and enabled 3d module.

    Highcharts.chart('container', {
        chart: {
            type: 'column',
            options3d: {
                enabled: true,
                alpha: 20,
                beta: 30,
                depth: 400,
                ...
            }
        },
        ...
    });

Live demo: http://jsfiddle.net/BlackLabel/nxwd3m2a/

Docs: https://www.highcharts.com/docs/chart-concepts/3d-charts