There are many websites and apps for checking train timetable info, transfer info and the current state of train lines, however if you try to find out general congestion levels for specific stations things suddenly get a bit harder.
Navitime offers congestion estimates on their website (Japanese only): https://www.navitime.co.jp/congestion/prediction/
However this feature has not found its way into their app, so if you’re mostly using your phone, perhaps save it as a bookmark and put it on your home screen if you’re going to be checking it frequently.
Navitime offers another feature which involves users reporting their station and line’s level of congestion along with any lateness of running trains. Unfortunately, this is another Japanese-only feature and is limited to the main Navitime app or another dedicated app called こみれぽ (Komi Repo, essentially ‘Congestion Report’). You’ll find it in the app store for both iOS and Android.
Finally, if you happen to be travelling on a Tokyu line (one of a few private underground rail service in Tokyo, separate to the main Tokyo Metro and JR lines), they provide their own app which can show you congestion levels at some of their stations. These levels seem to be determined by cameras pointed at ticket gates, which anonymises and uses the in-out count of people travelling through to determine levels of congestion - pretty clever! It not only graphs congestion levels per hour, but it also lets you view the cameras of the stations with the people anonymised. Unfortunately, this one is also Japanese-only, you can find it at the app store by searching for Tokyu or 東急線.