You can use the scatter3 function and specify the color for each one of your points. See the quick example below:
c = zeros(6,3);
data = [(1:6)', (1:6)', rand(6,1)];
% red if z greater than 0.5
c(data(:,3) > 0.5, 1) = 1;
% blue if z less than or equal to 0.5
c(data(:,3) <= 0.5, 3) = 1;
scatter3(data(:,1),data(:,2),data(:,3),[],c,'filled')
See the documentation for more details on using the scatter3 function:
Specifically, you can supply the value of c as a "three-column matrix of RGB triplets" as shown above, or define your own colormap and index into it.
