Yes. Yes he can. A Tailed Beast Bomb wouldn't do a thing to him. And if it has natural chakra in it, he can easily just dodge it or erect a barrier to block it.
Naruto can now use SM & BM at same time...
so this answer depends on what kind of Bijuudama we're talking about, cuz Naruto should be able to infuse his Bijuudamas with Senjutsu i believe