You could make a 2d plot of some kind whose color comes from the data in the 3rd dimension, e.g., a surface or a contour:
lat = -50:5:50;
long = -100:5:100;
altitude = 6000-sqrt(lat(:).^2+long.^2);
% first, a 3d scatter plot:
subplot(3,1,1)
[x,y] = meshgrid(long,lat);
scatter3(x(:),y(:),altitude(:));
xlabel('Longitude');
ylabel('Latitude');
zlabel('Altitude');
% second, a surface of the same data,
% colored according to altitude:
subplot(3,1,2)
surface(long,lat,altitude)
xlabel('Longitude');
ylabel('Latitude');
cb = colorbar();
cb.YLabel.String = 'Altitude';
% third, a filled contour of the same data,
% colored according to altitude:
subplot(3,1,3)
contourf(long,lat,altitude)
xlabel('Longitude');
ylabel('Latitude');
cb = colorbar();
cb.YLabel.String = 'Altitude';
