Navitime, Jorudan, Google Maps.

Hyperdia can still be consulted and offers a wealth of information, but check it first, don’t rely on it.

Even when Hyperdia was being updated it wasn’t infallible, and none of the 3 tools above are completely reliable sources either - for instance, I’ve found that the same system has given me information that is different to that of other posters here running the same search.

Also, as there are so many different rail companies in Japan there is no single answer for finding the timetables you’ll see at stations.