Obon is DEFINITELY the better choice. The only issue during Obon is that some trains can get sold out, so it's good to purchase tickets a few days in advance. But otherwise everything operates on a regular schedule. New Years is always very very tricky as prices go up a lot, things are sold out, and a lot of places are closed (museums, cultural sights etc). Even large parks can be closed over new years (Shinjuku gyoen).