Which means that you have to use the last syntax of plotyy to retrieve the handles to both axes and then feed it to ylabel. You can also set the labels as shown in the example (of the documentation).
An example with ylabel
figure
x = 0:0.01:20;
y1 = 200*exp(-0.05*x).*sin(x);
y2 = 0.8*exp(-0.5*x).*sin(10*x);
[AX,H1,H2] = plotyy(x,y1,x,y2,'plot');
ylabel(AX(1),'Something')
ylabel(AX(2),'Else')
