Some of the best value for money accommodations we've tried in Japan are from the Nishitetsu Hotel Group. This particular branch in Shinjuku is no exception with its well-kept rooms and superb location (2-minute walk to the nearest train station) which was a great jumping off point to the best sightseeing destinations and shopping areas in Tokyo.
Check-in is strictly at 3PM but in case you arrive early, you can opt to leave your bags at the lobby and explore the neighborhood or pay extra but still subject to room availability.
Travel maps and guides in major languages are readily available at the lobby free of charge, as well as some toiletries if you want to freshen up before heading out.
Real estate in Tokyo is precious so don't be surprised if your hotel with a 18sqm room is charging you an average of Php7500/night because its the convenience that you're really paying premium for. Also, most hotels in Japan have single and double/twin rooms only so booking for a family is a challenge unless you're willing to sneak-in your kids and fit yourselves in the tiny bedroom.
Apart from the usual room amenities, the hotel also lends a smartphone free of charge so you don't need to rent a portable WiFi or pay for ridiculously expensive roaming charges.
Pros: Clean and well-maintained accommodation, ideal location in Shinjuku (train station and shops are within walking distance), complimentary smartphones available for use in each room, and Shiseido toiletries in the bathroom.
Cons: Small room space and TV has no English cable channels.
Nishitetsu Inn Shinjuku
Shinjuku-Ku, Tokyo, Japan
Tel.: (813) 3367-5454