Iwata seem to be good but I only have experience of hakama buying. Try NOT to pay with credit card as they add an extra 5% onto the bill, on top of the consumption tax!
Another family run business in Tokyo is located at the exit of the Mita Line (subway) Suidobashi station. Just turn right! The shop is on Hakusan Dori opposite the Tokyo Dome Hotel and theme park complex. If you walk another 100m there is a Kendo/Iaido shop which also sells bokken, jo, videos etc.. Neither shop has a website. Walk a further 500m (approx) and you come to the Kodokan (Judo HQ).
I got a size 5 heavy gi for 10,000Yen (without belt) in December this year. They embroider your name on the gi top in katakana script for free if you ask (and you know how to write it) and will do your trousers if you ask again really nicely!
They also sell bokken & hakama.