I discuss recent advances using vNRQCD and SCET to study $J/\psi$ production in the transverse momentum dependent (TMD) framework. After introducing the different energy scales and hierarchies for quarkononium production in NRQCD, I consider the TMD factorization of production cross sections for $P_{T,\psi} \sim M_\psi \ll Q$ and $P_{T,\psi} \ll M_\psi \ll Q$. In the regime where $P_{T,\psi} \sim M_\psi \ll Q$ I show that the cross sections can still be matched onto the traditional LDMEs, which are used in the collinear factorization framework and I discuss recent results in this hierarchy. When $P_{T,\psi} \ll M_\psi \ll Q$, I show that soft gluon radiation (gluons with momentum on the order of mv $\sim$ 750 MeV) plays a critical role. In this region, the cross sections should be matched onto a new class of production operators, the TMD soft transition functions. I argue that these operators lead in the velocity powercounting and are critical for a correct description of production at low $P_T$. Finally, I present applications of this work for $J/\psi$ production at the upcoming EIC.