Your solution was very close. In fact you already had the logic worked out, you only needed to copy it from the text argument of the AddLabel() statement and apply it to the color argument.
Here it is after I made those changes:
# Percentage Distance Chikou/Close (26 days ago)
declare upper;
def price = close[26];
def chikou = Ichimoku()."Chikou"[26];
def pctPriceAbove = (price/chikou) - 1;
def pctChikouAbove = (chikou/price) - 1;
AddLabel(yes, "Chikou/Close %: " + if chikou > price then AsPercent(pctChikouAbove) else AsPercent(-pctPriceAbove), if chikou > price then Color.GREEN else Color.RED);