This app was mentioned in 4 comments, with an average of 1.75 upvotes
During your stay in Tokyo this app will save your life with regards to getting from A to B. It gives the name of the stops, estimated time of travel, how much the total trip costs.
I can recommend the Smile Hotel Nihombashi-Mitsukoshimae, in Chuo. It's a budget hotel but the accomodations are perfectly fine and you pay very little.
The hotel is very close to the Mitsukoshimae subway station, where the Hanzomon and Ginza lines stop. From Tokyo Station to the hotel is about 700-800 Yen by cab. You're a bit out of the way of the busy hustle and bustle of city life, but it doesn't take very long at all to get there by subway and the calm and quiet atmosphere is nice. From Mitsukoshimae Station to Tokyo Station takes about 9 minutes with 1 transfer, and costs only 170 Yen.
In the same street/area as the hotel is a smattering of small restaurants, two konbini (24-hr convenience stores, Family Mart and Daily Yamazaki), a barber and other things. I personally enjoyed breakfast at coffee house Mikado nearby the hotel (they serve breakfast until 11:00, whereas the hotel only serves breakfast until 9:30).
Be careful to look up the street address on a map beforehand as Google Maps only shows Smile Hotel Nihombashi, which is a different hotel from the same chain, 15-20 minutes away by foot. If you show the driver a map of the hotel area with a pin dropped at the hotel (that Tripadvisor link I shared earlier has a great map) they should have no problem finding it.
If you make reservations soon, it will cost you around $500 for 1 week (I took check in date to be 1st of September and check out date 8th of September since I don't know your actual dates).
Further tip: get the app Tokyo Subway Navigator. It'll save your life if you need to know exactly where to go and what lines to take.
Tokyo Subway Navigation is a great app I used while in Tokyo the past February that never failed me.
Here you go, I did a thing.
Word of advice: the view from the Skytree's upper deck comes with a surcharge (smaller than main admission price) that I would highly recommend you pay as the view from the top deck is truly amazing. There are also 2 photo opportunities that I found to be worth the small amount for getting your photo taken by a DSLR near some places well-suited for pretty pictures.
Also, if you have an Android smartphone, this app will save you a lot of headaches using the Tokyo Metro. For iOS, use this one instead.
In this app, your default view is of the full metro map, which you can zoom in on or tap a station and select whether to start from there or end there. You can also enter this on the top section of the app. Just Google what station is close to the destination you want, then enter that (as well as your departing station) into the app, and it will do all the work for you.