Both the Lagrangian and Newtonian method should result in the same equations of motion. The only difference is how you derive them. I find that Newtonian mechanics can be a bit more intuitive, however Lagrangian mechanics is a more systematic approach and therefore less prone for errors. Especially when dealing with systems with rotational motion, like your robot arm, Newtonian mechanics can be a real pain, so I would suggest Lagrangian mechanics. But you could always do both and compare the two to be more confident about the correctness of your model.