@joshuasosa,
Sorry, controlling the first label to display on the axes is not available as of now. However to display axis label for 0.0001, you can set the minimum value of y-axis to 0.00009
in this case.
axisY: {
logarithmic: true,
minimum: 0.00009,
maximum: 10000,
includeZero: true,
interval: 1
}
Also, check out this updated JSFiddle for complete working code.

—-
Manoj Mohan
Team CanvasJS