Toyoko Inn is an aberration that manages to stay in business despite its contempt for its customers. (77 out of 122 hotels in violation of building codes etc.) Think "Ryanair" meets Towering Inferno. I'm not entirely sure why homophobia got thrown into that ugly mix, but it did.

The Hilton will welcome you with the same high standard of hospitality that they provide to all guests. I have stayed at Hilton Osaka (a straight man - single room), which was simply terrific. IIRC, many Flyertalkers rate Hilton Osaka somewhat higher than Hilton Tokyo. (Of course, the Conrad in Tokyo is Hilton's top property).

Regarding Japanese attitudes to gay people in general. That's probably a topic for another thread. I'm sure that it could turn into a lively debate here - but you might prefer to rely on the accounts of people who have direct experience:
http://www.geocities.com/bjcjapan/roots.html