Why so sure about the eyes all of a sudden? Did you stumble upon anything more clarifying?
The only thing widely known, was that she supposedly has the same as eyes as Arkham (a hint to help us notice they are connected somehow before it was made obvious upon their meeting in the game) and that even the Jester form, cannot rid itself from those eyes - probably another hint to help us connect Jester with Arkham.
Each site says its own thing about the eyes. For example, the
Devil May Cry Wiki, says that Arkham has one blue eye and one brown. In
this very site, it's said that the eyes are red and blue. While in
Capcom Wiki, no mention of the colors appears.
The color might be uncertain unless you look at certain pictures of High Resolution like
this, which agree with what you say, but then come pictures of Jester like
this, which clearly hint to red and blue. I mean, forget the eyes for the moment. His whole Jester-Hat thing, while all the costume is purple, ends at one point at purplish red and the other at purplish blue. And since his eyes "flash" a bit more in this form, you can clearly see th blue at one of his eye. The other one can be something between red, light purple and/or brown.
I think it's safe to say the one eye is somewhat resembling to the color red - it can't be totally red since then it would be the color of Dante's trenchcoat, something between light purple/brown/red/maybe pink, or something like that. While the other is closer to a colour between blue and green, with again a small adittion of a light purple.