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Basically the best point value you receive are Hyatt properties.
Nothing else comes close with points to cash value.
That said, the Park Hyatt and Hyatt Regency are in Shinjuku.
If you are using Tokyo as a base to visit outside of Tokyo tourist sites, then the Park Hyatt and the Hyatt Regency are your best choices.
Most trains leave from Shinjuku.
The Park Hyatt closes in May 2024 for renovations.
For us, we generate lots of IHG points and the Intercontinental Tokyo and Kimpton Shinjuku are our favorites.
There is a new IHG Hotel Indigo, but it is very high on points and cash.
It is a brand new hotel.