I agree with Klaus that it doesn't make sense to set this on a per-y-axis level. It's really "x" and "y" in the sense of "horizontal" and "vertical", rather than "x-axis" and "y-axis". Some charting libraries (GViz) draw a clear distinction between these, but dygraphs does not.

How about "xPaddingPx" and "yPaddingPx"?