The proper way to do it is to use the ModelView matrix to move your object. The object's vertices are defined in the local space of the object, and it's generally good practice not to disturb the data.
This scales well to complex 3D objects and animation because the joint transforms and ModelView matrix operations can be done much faster in a shader than in software. Even if your scene is simple, it's good to adhere to the proper methods.
UPDATE: It's still ok to modify the ModelView matrix outside of the shader. For each object, this only means that we'll do 2 or 3 matrix-matrix multiplications per-frame outside of a shader, and then N matrix-vector multiplications inside the shader, where N is the number of vertices in the object.