I wonder what you have in mind when you say a ceremony at a venue. Are you going to bring with you a marriage superintendent, a Christian priest, a Shinto priest, or any other master of ceremony who can lead you in saying the words of vow?
And are you going to do the legal marriage in Japan, meaning you want your marriage based on Japanese law? I don't know your nationalities - neither of you seem to be residing in Japan, so if you are going to do that, and if neither of you is Japanese, you need to decide which part of Japan you want to register your marriage at, ask them if they accept that two non-residents to register marriage, and ask them what documents you need. Also if you are doing that, you need to think about the sequence of events - you do the vow at the ceremony, then go to the city hall to register (you need two witnesses), what do you do with the guests? Do the guests need any translator/interpreter during the event, or are they ok with English?
Also if you just want to do the ceremony of vow, as I said you need to decide on the style, which pretty much determines the venue. Shinto ceremony requires a Shinto shrine/attached venue, or Christian ceremony requires a chapel.
Even with seeminlmgly simple thing as booking a venue like the one suggested (which I admit is a nice location) you need to book early, pay at latest 15 days in advance. Also it is a Japanese style location, where you sit on the floor. No chair and table. They will provide hot water and tea making equipment, but you need to bring the tea and other drinks (no alcoholic beverages allowed). If you are going to go there from your hotel, would you require makeup and dressing service? Any car to take you there?
I guess that is what a wedding planner is there for.
If neither of you have a strong connection/interest in Japanese culture, I might say Japan is not really an easy location as wedding destination.
One example inKamakura, Shinto style. The Japanese page mentions a fee of 200,000yen, which is just the fee to the shrine, so excludes the dresses and any extra.
http://www.tsurugaoka-hachimangu.jp/shinto_is/shinto_wedding.html