I don`t know about Tokyo, but there is a small Vietnamese community near me. Or at least there appears to be one - there are 2 small restaurants run by Vietnamese families and a small (very small!) corner sort of shop selling foods from Vietnam all in the same small area.
I would imagine that there is enough of a community to keep the shop alive...
I am going to guess that there is a larger community in Tokyo, but as you say, finding it may be difficult. You might try looking around for Vietnamese restaurants that are "authentic" (run by real Vietnamese) and asking there. The owners will have likely been in Japan a long time and will have a lot of connections.
Good luck - I hope you are able to find a community for support.
ETA; Here is a link you might want to check.
JVCA 財団法人 日本・ベトナム文化交流協会