You can calculate the bin averages pretty quickly using discretize and accumarray:
Some sample data:
npt = 10000;
A = [rand(npt,1)*180-90 rand(npt,1)*360-180 rand(npt,1)];
5-degree bins:
latbin = -90:5:90;
lonbin = -180:5:180;
nlat = length(latbin);
nlon = length(lonbin);
Use discretize to figure out which latitude and longitude bin each point falls into, then convert the row/column indices into a single array index.
ilat = discretize(A(:,1), latbin);
ilon = discretize(A(:,2), lonbin);
idx = sub2ind([nlat nlon], ilat, ilon);
Use accumarray to average the values assigned to each index, then reshape to a grid:
altg = accumarray(idx, A(:,3), [nlat*nlon 1], @(x) mean(x), NaN);
altg = reshape(altg, nlat, nlon);
Finally, plot:
pcolor(lonbin, latbin, altg);
