The room can accomodate three easily. In
comfort will be based on your state of mind.
Rooms in Tokyo in particular are smaller
than the rest of Asia and US. Twin is twin.
I can tell you for sure that the Hotel will
mind if they knew. Might I suggest that
upon arrival one of you take a seat in the
lobby (huge) and enjoy the people watching.
Two of you go and check-in. Have your bags
taken up to the room. Come back down and get
your other roommate. Also to save money
explore the area. There are a number of fast
food (American style and Japanese) in the
area to serve the numerous office buildings.
Take the underground walkways to various
shops. The Hotel is also close to the
famous Shinjuku electronics area. Enjoy!