IHG ANA Crowne Plaza/Holiday Inn is a good choice as you can use your points worldwide.
We were Mitsui members and used the points for breakfast coupons.
Richmond hotels has a programme in which you can use the points for a rebate on the roomrate.
Daiwa Roynet is an option: we have some points in our account but did not use them yet.
JR Hotels is also an option.
There are more, but those have an English language website and accept addresses outside of Japan.