I am sure you will enjoy your time in Tokyo. There are plenty of places to find perfumes, but to stock up or not is dependent on a few things.
#1 Exactly what are your favorites ? Some perfumes are simply not available in Japan. Clinique Aromatics, Zen by Shisheido, and Youth Dew by Estee Lauder are not to be found in Japan. I am sure there are others, but of those 3 I am certain.
#2 Are you a military dependent or an expat ? If military, you have base shopping to help you in your quest.
#3 Duty and import restrictions are placed on the amount and type of perfumes you are allowed to bring into the country.
Perfumes are $$$ here, and as a previous poster said, there are no Marshall's or anything like that. However, in Kichijoji, a busy and bustling suburb in west Tokyo, there are several small kiosk type operations that do sell perfumes at a discount. They seem t specialize in end lots, gift sets, etc.
There are also department stores like Ito Yokado, a national chain, which have small, but affordable brand perfumes as well as some japanese types.
I was told by a Japanese perfumer by the name of Satori, whose lovely shop was mentioned here on another thread, that Japan is not a country that uses perfume. If I can judge by the smell of the people with whom I am regularly shoved into the train carfrom Shinjuku, they do not use scent. I fact, they do not even seem to have a personal body scent - not odor- but just a personal smell. They smell of nothing.
The exception to this are the drunken salarymen and old men coming from the racetrack, who reek of cigarettes and cheap beer.
I work at an American school, and feel free to use perfumes at my discretion. I have scents in my classroom and my students have perfumes they prefer over others, commenting when I make a change.
Feel free to contact me when you arrive, and I will happily show you a few good places to sniff about. I will be here until the summer.
PS ... Don't forget about duty free shops before you leave the USA.