It depends on direction. In the mornings from Shinjuku towards Iidabashi and Kuramae and from Daimon toward Shinjuku (the route you'll be taking), it's usually not too crowded in my experience. From Hikarigaoka to Shinjuku and on to Roppongi (and from Iidabashi to Shinjuku) it can be pretty crowded, though not to the degree of other lines (like the Ginza, Marunouchi, or Tozai lines).