Picking a specific mini and\or costume could have been a challenge. After all, he did have about sixty different figures to choose from.
Thankfully, Reaper Miniatures made things a little easier with their totally-not-a-Joe figure Cobra, Modern Ninja (50082).
For my version of Snake Eyes I based it mostly of the Renegades version of his costume, as opposed to the all black original. The visor is a little different, and my ham-handed attempt at making knee pads with green stuff didn't work too well, but I think it came out OK.
Another possible option, if you want a slightly more dynamic pose, would be the Heroclix Black Tarantula figure: