Churches

Hi Kayla, here, I found many churches where they do Mass in english in Tokyo, I hope one of them is near you:

1- Toshima: http://tokyo.catholic.jp/english/churches/tokyo-en/16589/
2- Takanawa: http://tokyo.catholic.jp/english/churches/tokyo-en/16564/
3- Umeda: http://tokyo.catholic.jp/english/churches/tokyo-en/16612/
4- Shimura: http://tokyo.catholic.jp/english/churches/tokyo-en/16534/
5- Roppongi: http://tokyo.catholic.jp/english/churches/tokyo-en/16509/
6- Meguro: http://tokyo.catholic.jp/english/churches/tokyo-en/16481/
7- Kojimachi: http://tokyo.catholic.jp/english/churches/tokyo-en/16443/
8- Koiwa: http://tokyo.catholic.jp/english/churches/tokyo-en/16438/
9- Kasai: http://tokyo.catholic.jp/english/churches/tokyo-en/16401/
10- Asakusa: http://tokyo.catholic.jp/english/churches/tokyo-en/16353/

About famous churches, I'm not sure, hopefully someone else can help with that one !
I hope this helps! :-)

Oh, here's a website listing many Catholic Churches in TOkyo and other cities:
http://tokyo.catholic.jp/english/churches/

I checked all the ones in Tokyo to see which ones did Mass in english, but I didn't see the other cities. If you need, please take a look! :-)

I have personally been to this one with my wife in Matsudo, Chiba prefecture:
http://tokyo.catholic.jp/english/churches/chiba-en/16471/

It was a little bit difficult to find but it was nice

The most famous churches would be the Urakami Church in Nagasaki and the numerous churches on the Goto islands of Nagasaki, which the government is in the process of trying to get registered as a World Heritage site.

 http://www.visit-nagasaki.com/spots/detail/211

https://www.jnto.go.jp/eng/regional/nagasaki/goto_islands.html

In Tokyo , the Sekiguchi Catholic Church 

http://tokyo.catholic.jp/english/churches/tokyo-en/16544/

and the Kojimachi Catholic Church also mentioned in Rodrigo's reply are relatively well known.