G = rand(5000, 3); % "data points" is not clear
N = 100;
siz = size(G);
GG = reshape(G, [N, siz(1)/N, siz(2)]);
R = reshape(sum(GG, 1) / N, siz(1)/N, siz(2));
If the length of the first dimension is not a multiple of N, you might want to crop the input at first.
R = BlockMean(G, N, 1) / N;