They used to have a rate about 3000 yen for a day. I've just looked at their English web site, but I couldn't find mention of visitors. The text on the English site says:
A person wishing to learn Aikido at Hombu Dojo is requested to register himself/herself as Hombu Member. Fill out the form available at the reception office, pay the registration fee and receive a membership identification card. Present the membership card at the office before every practice and pick it up prior to leaving. The office is open daily except Sunday afternoons and holidays.
Registration Fee (non-refundable)
I presume that you would have to pay the daily rate in addition to the Aikikai membership. I'm sure some of the other non Aikikai guys that post here have trained at Hombu as visitors, maybe they can provide more info.