If you plan to go to Kyoto I can recommend www.tozando.com
. They do good work. If you order and pay your items up front they can even mail it with "Black Cat" to your hotel/ryokan so that it will be ready for you once you get there. They have a basic aikido gi which I like a lot. They are a bit big however until you get them washed.
Also they have great hakamas. For traveling a tetron hakama may be what you are looking for. The cotton ones wrinkle quite easily.
BTW: where are you going to stay in Tokyo? Allow me to suggest www.kimiryokan.jp
. The owner there it a nidan in Aikido (I think) and it's a great place to stay at a very reasonable price. It's in Ikebukoro and it's quite convenient to get to hombu dojo from there. Get a railpass
Have a great trip