We went to Japan for Spring Break last year. DH, me, and sons ages 13,11,9. Fantastic!!! We traveled by train and subway all the time and had no trouble. We did tend to not be on during rush hours, but it wasn't ever that crowded. We saw the "Honorable Pushers" but it was never crowded enough for them to have to push anyone in.
Have you vacationed in other countries? I would say Japan would be really hard as a first overseas visit. The language is a problem

and the culture shock is pretty major

We've traveled to many places and we were overwhelmed at first. The first evening was the most challenging, partly because we were exhausted. We took the train from the airport to a station near our hotel. We tried to get a taxi to the hotel, but never could communicate well enough

so we walked. It wasn't bad, about 10 minutes, with luggage. Then we were going to eat dinner in the hotel and it was CRAZY expensive, so we headed out the door in search of a restaurant. Oh, this was in Osaka, by the way. Anyway, there were lots and lots of restaurants, but we were too intimidated to go in! So many were tiny, our family of 5 wouldn't fit. Lots had the plastic food models outside, but no English menus. We finally went to an Outback Steakhouse! Felt like a total cop out, but necessary at the time. The next day we successfully mastered the Japanese Restaurants.
Oh, ATMs are tricky. Most are not compatible with cards from the USA. The ATMs in the post office ARE! So plan accordingly! Even at
DisneyLand Japan we couldn't get the ATM to work!
We loved it

Feel free to ask any specific questions!
Katy