To get to Takadanobaba, it's a lot easier to take the Yamanote line from Shinjuku. The subway goes there too.

The main things I remember in Takadanobaba are the Wendy's (notable solely because it has a huge mural of the Stanford University Quad inside), the "Fiddler" pseudo-English pub a bit further down the street from Wendy's, and Ben's Cafe which occasionally features stand-up or improv in English. It's not a bad area, it does always seem to be full of students just hanging out.