Why not both? JK
I think it really depends on what kind of game you are going to do and specialy how skilled you are on both sides.
One major point is how familiar people are with 2D tools against 3D tools. Everyone has used MS Paint one, everyone has heard of photoshop and so on. But when it comes to 3D most people only heard of Blender or Maya which can be kinda intimidating for newcomers. More accessible 3D tools are harder to find, so here are 2 tools for voxel art (think of it as 3D pixel art) that can help MagicaVoxel and Goxel.