We stayed in Shinjuku at the
Century Southern Tower which was so very convenient and wonderfully nice for about $200 a night. The rooms were good size with a nice view and the Shinjuku Station is very close by. If possible, you want to stay on one of the areas near the main loop of trains through the city. Shinjuku is one of those and also is a direct shot to Ghibli. Disney was also very convenient. We did not stay at a Disney hotel because they are so damn expensive and, getting to the Parks from Shinjuku was quick and easy. I would stay there again in a heartbeat.
Also, the hotel is right across from one of the best stores in Tokyo - Tokyo Hands.