Using InstancedMesh would be reasonable enough, too. But 3500 meshes is too many draw calls, with one per mesh.
Aim for something like <100 draw calls and <100,000 vertices if you can. Using InstancedMesh will reduce the draw calls to only one draw for all instances, but does not reduce the vertex count compared to drawing spheres individually. Using sprites or points will reduce the vertex count compared to spheres. You could use some combination of those, if needed.