I have confirm tickets from 16-21 June with KA for $1988/person inclusive.
I used to stay in a Ryokan in Ikabukuro but they are full.
Since I will go to Thomas Land and Disney Land I think Shinjuku is quite convenient and it seems that the rooms there are quite spacious according to the description from the net.
Well actually it will takes about 14 minutes on foot but they have shuttle service between Shinjuku Station and hotel on every 20 to 25 minutes.
Althought the last bus from station to hotel at 10:30pm I don't see I will go back to the hotel later then that because I am taking my son, also we could go for night walk in Shinjuku (Watches, drug stores etc) after he has taken his bath and had is dinner.