Budget
Ten Ten Guesthouse
The cheapest youth hostel in Tokyo. Don't expect too much for the price. Cockroaches & Bed Bugs included. The manager manages 6 of these guesthouses, all the same price, same style.
Tama Ryokan
There is a lounge for relaxing and internet access. Three-minute walk from Takadanobaba Station.
Tokyo International Hostel
Located on the 18th and 19th floors of a high-rise in Shinjuku, with great views over the city including a hot tub and baths overlooking the lights and skyscrapers of Shinjuku and comfortable rooms.
Sakura Hotel Hatagaya
Just 2 stations 3 min. to Shinjuku. Affordable hotel accommodation in central Tokyo. Staff can speak English.
Green Plaza Capsule Hotel
Not a bad capsule hotel, though it runs a little more expensive than most of its kind. They will take foreigners as long as they don't make fools of themselves. Remove your shoes on entry.
Manboo Internet & Comic Cafe
Internet cafe that has small, private rooms to crash out in. Rooms have a comfortable reclining chair or a "flat seat" option, internet, TV, and headphones. Free soft drinks and coffee are provided and there's also a shower room/toilet and toiletries on sale.
Ace Inn Shinjuku
Capsule Hotel near Akebonobashi Station. On the ninth floor there is a common space with vending machines and TV, where you can meet with the other guests from all over the world. Internet connection via WiFi in the whole building or PC on the ground level is free. English speaking staff.
Midrange
Hotel Sunroute Plaza Shinjuku
Includes a restaurant, a bar, and massage parlor. Located just 2 minutes walking from Shinju-ku station south exit. Recommended for taller guests. Better rates are often available by the usual Western online booking agents.
Hotel Sunlite Shinjuku
Shinjuku Prince Hotel
Includes restaurants, a bakery, and salon.
Tokyu Stay Yotsuya
Part of the Tokyu Stay chain, these hotels are popular with business travelers. The small kitchenettes, washer/dryers, and free LAN access in all rooms makes these a good value.
New City Shinjuku
Located in a tranquil spot across Shinjuku Central Park from the Tokyo Metropolitan Government building, this hotel has clean rooms with nice views of the skyscraper district, two decent onsite restaurants for the truly lazy, and a free shuttle bus to and from Shinjuku station.
Top end
Park Hyatt Tokyo
Towering above the rest literally and figuratively, this hotel is best known for featuring prominently in the movie Lost in Translation. Surprisingly intimate in feel, one of the standout features is the 47th-floor "Club on the Park" pool with floor-to-ceiling views of Shinjuku at night. Service and amenities are superlative, but rates are astronomical even by Japanese standards.
Keio Plaza Hotel
Less than 10 minutes by foot from Shinjuku Station, has rooms that face the Shinjuku Metropolitan Government office.
Hyatt Regency Tokyo
744 rooms and suites with views of Mt Fuji and Shinjuku Central Park. Regency Club lounge for free continental breakfast, tea service and evening cocktails. Hosts a roof-top pool and healh spa.
The western side of Shinjuku has a notable concentration of luxury hotels.
Sakura House
If you plan on staying in Tokyo for a month or more you might want to check this place out.