Accommodation in Tokyo
Hey there!
Finding an accommodation in Tokyo is a cake-walk, considering that there are millions of places spread out to cater to the business and pleasure tourists coming into the prefecture everyday!

Tokyo Bay (Source: orangeandmilk)
However, here are my recommendations according to your specific needs of centrally-located yet cheap and clean accommodations. Read on.
Hotel Business Villa Omori
Address:143-0015 Tokyo, Ota-ku, Omorinishi 3-32-7
Rates: Single Room - US$54.57
The Hotel Business Villa Omori has the best location possible - what with it being a mere 5-minute taxi ride from Haneda Airport, apart from being just a 5-minute walk from Heiwajima Train Station, and only 2.5 km from JR Omori Train Station!
Apart from the standard facilties that will make your stay a pleasant one, added amenities include a free-use internet station in the lobby and free Wi-Fi.
The staff are very friendly, and though they may have some issues with the English language, they do successfully communicate with you and sort out all your issues perfectly! I'm sure you'll have a good trip.

Hotel Room (Source: nachof)
Though most reviews I found online were in Japanese, they all seemed to concur on the fact that it is among the cleanest and cheapest hotels in Tokyo! Here's what a traveler had to say:
Easy access from Haneda airport, good location. The room is small but clean and complete though. Would recommend to friends who touch down late at night from haneda airport as it only takes 30 mins train and 5 mins walk from station to hotel.
(Source: Villa Omori, Guest reviews)
Horidome Villa Hotel Tokyo
Address: 103-0012 Tokyo, Chuo-ku Nihonbashi Horidome-cho 1-10-10
Rates: Single Room - US$75
A 30-minute drive from the Haneda Airport, and quite close to the Tokyo Stock Exchange, the Horidome Villa Hotel Tokyo is one of the better options. Though it comes for as low as $75, you will be pleased with the amenities offered, which include high speed (wired) Internet access, a plasma TV in the rooms, apart from laundry services and luggage storage facilities!

Plasma TV in cheap hotel room! (Source: mattbuck4950)
Here's what someone who had a pleasant stay at the Horidome Villa Hotel Tokyo had to say:
Our stay was great! The hotel met our every need and very clean as well which is always an added bonus! Tight fit for 2 people but we were only there to sleep anyway. However, very good value for the low price. Hotel staff was helpful and spoke enough English to communicate. Great location as well in terms of subway... Close to a stop which made all other areas easily accessible. The location is excellent and above all, the staff was really helpful and accomodating. Would recommend this hotel to anyone looking to save a few yen on accommodations.
(Source: Book now!)
I hope these hotels suit you in every way, and fit your specific needs. Do have a great stay in Tokyo!
If you want to find out the best nightlife venues in Tokyo, or want to know the intricacies of subway-travel in this prefecture, do get in touch with us and we'd be glad to assist.
Till then,
Happy Planning!
Rohini
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Asakusa Hotel Fukudaya
Address: 111-0022 Tokyo, Taito-ku, Kiyokawa 1-35-11
Rates: Standard Single Room - US$33.11
The Asakusa Hotel Fukudaya would be one of the most ideal lodging options for you, considering your budget and your location requirements. A 12-minute walk from the Minami Senju Subway Station, Asakusa Hotel Fukudaya is located ideally. Apart from that, the facilities offered are up-to-the-mark, and the staff are quite accommodating.
hotel fukudaya (Source: romana klee)
Though the picture may make you feel it is a bit run-down, don't worry, since many previous travelers have recommended the Asakusa Hotel Fukudaya! Here is one such review that I read online:
(Source: Booking.com)