JR East Tokyo area commuter train operations are back to normal.
It is now safe to use Hyperdia to plan JR-only trips within Tokyo, 
Kanagawa, Saitama, Chiba and Gunma.

http://www.hyperdia.com/

Still not normal: Tohoku Shinkansen, Joban Line Ltd. Express and long 
distance runs (north of Hitachi City) and Tohoku Line north of Kuroiso.