Presenting a small, nicely wrapped, item as a gift might well be understood better than a tip.
The only time I have ever left a gratuity of any type at a hotel in Japan was a few years back. I offered to buy dinner for the whole staff of a hotel at which I stay regularly. When I told the GM of the hotel what I was thinking, he combined it with the annual employee dinner and it turned out to be a heck of an event for me and my family as well as the staff.
Rather more pricey than a normal gratuity, however.