Best hotels near Tokyo JR lines

I'm staying in Tokyo from August 8th til the 12th. I've been looking around for places between 5000 and 10000 yen (closer to 5k preferably). The problem is the hotels I've found are situated closer to stations run by private train companies. What are the best economical accomodations near the JR lines for a pass user? Yeah I know the 8th is very soon, but I stayed in Aomori for the first 4 days of my vacation and only checked for hotels there.

P.S. I plan to stay at a capsule hotel for at least one night. Probably Shinjuku Green Plaza unless anyone has better suggestions.

You have so many damn choices,
I can think of a few already,
I�@Stayed at nishi-shinjuku Hotel.
It's cheap, but the rooms are small,
It's only about ‚T�@Mins away from a JR�@Station.

There are closer ones such as Prince Hotel and Kent Hotel.
they are all close to the JR
Station

I've stayed at the Shinagawa Prince Hotel before. It's nothing fancy, but it is across the street from the Shinagawa station. A 2 minute walk. Very convenient.

There are hundreads of hotels in Tokyo and nobody but you knows which is ''the Best'' for you.

Even in case all the hotels are booked out, you can spend a whole night at an internet cafe or a capsule hotel.

Do I understand your problem is the price in combination with near JR? For tomorrow you can still book a room at Star Plaza ( New Star full ) Ikebukuro at Yen 7350. http://www.star-hotel.co.jp/
It is walking distance from JR Ikebukuro station. Business hotels at Shimbashi area or Ginza area are around Yen 9000 to Yen 10 000. Another area to check is Kanda.
If you decide for Ikebukuro there is a capsule called Ikebukuro Plaza Capsule and Sauna.
Shinagawa Prince single at Main tower starts at Yen 10500 for Price Club member and includes breakfast.

Yeah my problem isn't a lack of options, but not knowing what options I have. I didn't want to get off at a random station and start walkin around with my luggage aimlessly lol. I still need to narrow it down.
Currently Ginza, Ikeburo, Akihabara, and Shinjuku are my prime choices.

Although I'm a fancy free lone traveler, I just wanted to know which one garnered the most satisfaction for its price.

I prefer not to stay at an internet cafe unless I have to. Thanks for your input guys.

Spooferanies,

You ought to look into the Toyoko Inn chain of business hotels. They are clean, cheap and always close to stations. The downside is that it may be hard to book rooms at short notice due to their popularity.

For tomorrow:
Shinjuku Washington at Yen 12000 higher than what you wanted.
Akihabara Washington full
Shimbashi Unizo ( former Sun ) full

Well worst case scenario has happened. I'm wandering around aimlessly again lol. Time to do this guerilla style and just hop on and off the Yamanote line until I find something.

Hotel Mets Mejiro is very close near by Mejiro Sta.
http://www.jrhotelgroup.com/eng/code/codeeng125.htm

Hotel Sunroute Takadanobaba is 1min walk from Takadanobaba Sta.
http://www.sunroute.jp/HotelInfoSVE

Spooferanies,
Where at least did you get a hotel room? Just curious/interested how it ended. Sorry

Well after traveling around the Yamanote line for a bit, I stopped at Shibuya, Shinjuku, and Ikebukuro. I couldn't find visible hotels for the life of me. Just lots of disorienting lights.

It was getting late so I ended up in Ueno. After a bit of travel, I ended up at the first hotel I could find which was Hotel New Ueno. Single rooms for 8,900, pretty expensive for the size of the room that I got. However, the staff was friendly. I didn't stay for too long because of my first impression of Ueno. Lots of homeless, and not much to do once you see the park.

Finally I decided to find a Toyoko Inn that was actually vacant (hard to do with short notice). I chose the inn at Bakarucho for my homebase for about 5 days since then.

I had an easier time in Aomori. There was a hotel called Hyper Hotel Passage for about 1k less yen than Toyoko with the same amenities. Nice place.

Well after traveling around the Yamanote line for a bit, I stopped at Shibuya, Shinjuku, and Ikebukuro. I couldn't find visible hotels for the life of me. Just lots of disorienting lights.

You didn't look at maps beforehand or research any of the forementioned hotels? There are hotels within walking distance of all these places.

I did lol, I just couldn't find em.

Star Hotel Shinjuku. You can see it from the east exit. Just under 10,000yen a single.

http://www.starhotel.co.jp/city/tokyo/guest/e-standard.html

Vintage Shinjuku Hotel

6100yen
http://www.japan-hotels.net/344-Vintage-Shinjuku-Hotel.html#bookNow

I stayed in Hotel Strix, very very near JR ikebukuro line.
nice clean rooms, plus relatively reasonable prices