I have stayed at the grand hyatt and the Pen twice each. While the GH is not considered one of the best, I would highly recommend the Pen. Also, for whatever reason, whenever I am going to Tokyo, the Pen has the best rates, which help seal the deal. For example, I am going in May and have booked an executive suite at around $500 per night, whereas at the other hotels you mentioned, that is close to the price for a base room.