I googled both in English and Japanese, but couldn't find exact location where this scene with Misato, Asuka and Rei standing in a crowd was filmed. So, I registered on this forum only to post the result of my personal investigation.
TL;DR: 35°40'05.3"N 139°36'00.5"E Chitose-karasuyama station, Setagaya City, Tokyo
Investigation details:Starting point is あかしや [akashiya] advertising signs on the poles along the street. I can recognize the first (千)[sen] and the last (山)[yama] small Kanjis that written below, but because of low video resolution Kanjis in between absolutely not readable. Last one I assume is (駅) [eki] (station) that make sense. So, all we need is to find station in Tokyo that name starting with 千 and ends with 山 with two complicated Kanjis in between.
I also watched that video posted above, where Hideaki Anno filming this scene, on 14:49 you can see the same あかしや advertising and on 14:53 you can see the train arriving. A lot of time passed since 1997 and everything changed here in Tokyo... Except trains! I immediately recognized Keyo line (京王線) train with dark red stripe. So, let's inspect this line for our station. It took not much time, just few stations from Shinjuku we found it. Chitose-karasuyama staton! (千歳烏山駅) exactly what we looked for! Let's go to Google street view.
We are searching for "classic" Japanese narrow street with a lot of shops near the station. On original movie frame we also can recognize 南烏山 6-4 (of course, only "6-4" is somehow recognizable, but since we know the location, everything come in place now) so, 6-4 is northen side from station, and there is one long and narrow street. On Google street view we can change the date when photo was taken. Earliest possible date is July 2009. Still very far away from 1997, but better than October 2022. There is no more あかしや, but we can see a lot of other similarities with movie scene. E.g. blue advertising sign 京王メガネセンター (Keyo: megane senta:] is still there! That is it. Case closed.
