$100 per night for 2 adults within a reasonable walking distance from Tokyo station is impossible (the tanking US$ is just making things difficult). By "reasonable walking distance" I mean walking distance that an average person can comfortably cover with checked-in luggage.

However, if you are willing to have your luggage delivered to Kyoto directly (ie. you don't have to carry your luggage from the Tokyo station to your hotel), then you may have a chance of finding something within this budget (for hotels slightly further from Tokyo station).

Alternatively, I suggest you consider staying close to the JR Shinagawa station. Shinagawa is the second shinkansen stop (after Tokyo). Hotel prices are much, much more reasonable there and Shinagawa station is less confusing than Tokyo station. Consider the Toyoko Inn at Shinagawa-eki at Takanawaguchi. As shown in the map, from Shinagawa station, take the Takanawaguchi exit. YOu will see a major street immediately. Make a left on this street. After about 2 minutes, you will see Tokyoko Inn across this street.

http://www.toyoko-inn.com/e_hotel/00029/

At Shinagawa station, you will find a Dean & Deluca, a bunch of food shops inside the JR station, and two supermarkets right outside the Takanawaguchi exit.

For the shinkansen, you should reserve your seats in advance. I think it's free if you use your JR Rail Pass.

http://www.pearlhotels.jp/en/yaesu/index.html

5 minute walk from Tokyo station and very close to $100/night...just a little over.

http://www.hvf.jp/eng/

Otemachi, Hatchobori and Nihombashi are all in the vicinity of Tokyo Station.

Villa Fontaine is a nice chain. However, from JR Tokyo station, you'd need to take a cab to get to any of these three properties listed above, assuming you have checked-in baggage. The cost of two such cab rides (roundtrip) will offset any benefits you may get in reduced room rates.

Toyoko Inn near Shinagawa may fit but it's very difficult to book a room at this location. You need to book ASAP. Your budget is extremely restrictive for Tokyo and even Shinagawa for two people. You might have better luck staying at Shin-Yokohama if you are expecting US$50/person double occupancy.

>>Villa Fontaine is a nice chain. However, from JR Tokyo station, you'd need to take a cab to get to any of these three properties listed above, assuming you have checked-in baggage. The cost of two such cab rides (roundtrip) will offset any benefits you may get in reduced room rates.<<

Generally, Otemachi, Hatchobori and Nihombashi are considered in the Tokyo Station Area. They are all close to JR stations.

Otemachi branch -> Kanda Station

Hatchobori -> Hatchobori Station, however transfer from the Sobu Line to the Keiyo Line at Tokyo is terribly long.

Nihonbashi -> Shin-Nihonbashi

All these stations are next to Tokyo.

If I dare to say, your hotel suggestion regarding Shinagawa is out of the range in terms of the OP's location request. I'm afraid your comment to my suggestion sounds somewhat nitpicking.

Having said that, budget-wise, the OP might consider staying in Shin-Yokohama, as route-san suggests. The 6:00am Hikari originating at Shin-Yokohama arrives at Kyoto at 8:01. Then all Hikari and Nozomi trains stop at Shin-Yokohama.

Relevant thread: http://tinyurl.com/67x5tt

If you don't use the Japan Railpass as soon as you arrive in Japan, or you don't use it at all, you could utilize the 'Suica and NEX' combo.

www.jreast.co.jp/e/suica-nex/index.html

NEX timetable: http://tinyurl.com/3hh4no

Train schedule search: www.hyperdia.com/cgi-english/hyperWeb.cgi

Yaesu Terminal Hotel is a nice business hotel that I had stayed at, but it costs around US$140. It is just 2 minutes walking from the east side of the station.

This is also an N700 train set which is normally only used for Nozomi runs. I am occasionally tempted to stay in Shin-Yokohama for this reason when I have a JR Pass.

<<<The 6:00am Hikari originating at Shin-Yokohama arrives at Kyoto at 8:01. Then all Hikari and Nozomi trains stop at Shin-Yokohama.>>>

If all you are looking for is an inexpensive place to crash before heading to Kyoto, here is something we've done a few times: overnight at Hotel Sky Court Narita (http://www.skyc.jp/hotel/english/narita/). It's near Narita airport with free airport-hotel-airport transportation (call box at the airport drive-through-transport pickup area; look for a sign). Nothing fancy and not a tourist location; the room is basic (i.e., small), clean, with in-room toilet and shower, the price is in your range, there is a restaurant with decent food, and staff were very efficient. They take online reservations. Staying there enabled us to relax and energize after the long flight from O'Hare without the hassle of navigating into Tokyo the same day. We would arrange transportation details (rail passes, train reservations, etc) and currency exchange/withdrawals at the airport before heading to the hotel. We took the hotel transit back to the airport the next morning and headed straight for the train to continue the journey. The most straightforward train itinerary from NRT to Kyoto appears to be Narita EXpress to Shinagawa and transfer there for the Shinkansen to Kyoto. FWIW. Have an enjoyable trip.

The more I think about it, the more I agree with Route's suggestion to stay at Toyoko Inn at Shinagawa if possible. The hotel is near the train station, and Shinkansen to Kyoto goes through Shinagawa. Use the NEX-Suica combination ticket to save money and break the journey from Narita - Shinagawa - Kyoto into more manageable (shorter) sectors instead of one long train ride.