Hotel suggestions

My first time visit to Japan and travelling alone.
I am staying in Tokyo for 6 nights (day trips to Yokahama, Hakone etc) what would be the most comfortable hotel yet 5-10 mins from a train station. I have read the reviews for Century Southern Tower which sounds okay and Keia which can be iffy what about in other areas such as Ginza or Akihabara, or is Shinjuku the best central location.
I am willing to pay for the extra comfort if it would make the trip a more worthwhile and enjoyable experience.

Your suggestions for places to stay in these other areas would be a great help as would the proposed itenerary

2 nights in Nogoya...Toyota etc
4 nights in Kyoto
1 night in Miajima
2 nights in Kanazawa
2 nights in Takayama
2 nights in Matsumoto
2 final Nights Tokyo

This is probably the best forum I have run into when planning a trip..many thanks...

The Century Southern Tower is, indeed, very conveniently located. I recommend it if a convenient location is important to you. And it is a nice mid-range hotel in other respects as well.

2 nights in Nogoya...Toyota etc

The Marriot is difficult to beat in terms of location and comfort:
http://www.marriott.com/hotels/travel/ngodt-nagoya-marriott-associa-ho...

4 nights in Kyoto

The Granvia Kyoto:
http://www.granviakyoto.com/

Or APA Hotel Gion:
http://www.apahotel.com/~language/en/hotel/kyotogion/index.html

1 night in Miajima

I cannot recommend the Iwaso. Unfriendly, unsophisticated service towards - at least - foreign visitors. I liked the Arimoto Grand Hotel:
http://www.miyajima-arimoto.co.jp/english/

2 nights in Kanazawa

The ANA and JAL hotels next to the station are convenient.

2 nights in Takayama

The Best Western in convenient:
http://www.bestwestern.co.jp/english/takayama/

There are also some nice ryokan.

2 nights in Matsumoto

A wide range of average business hotels, but nothing outstanding.

I just visited Kyoto for the first time... Uji already recommended it, but Granvia Kyoto is a must if you're going there, especially if it's the first visit. I can't stress it enough. Simply can't beat its convenience (stores, shops, restaurants, right on top of the train/bus/subway stations). The place is massive, almost a sightseeing spot on its own. It's not the cheapest, but I found it to be a bargain for what you get in return. I'm definitely staying there again next time.

In Tokyo, I stayed at Hotel New Otani Tokyo. Great service and a nice view of a garden with small waterfall. The hotel is made up of two connected buildings, the main and the garden tower. I stayed at the latter, as it was cheaper and still offered the same services as the former. It's fairly close to JR Yotsuya station, which gives you quick access by train to many areas of Tokyo. http://www.newotani.co.jp/en/tokyo/index.html

Hyatt Regency in Shinjuku is nice, but everyone speaks english there so it isnt much of a japanese experience. I personally wouldnt stay in Shinjuku again, though, I didnt like it much at all. I'd rather look to somewhere around Ueno. For Kyoto, the Brighton is beautiful and reasonable, but a little away from most sites (except the Imperial Palace), the Westin Miyako is great, but not handy to the train station, and the Hyatt is brilliant, but pretty expensive on weekends. For the area and price, I would recommend trying a night or two at the Westin. I also recommend the Grand Hotel Arimoto at Miyajima. It is very special, and worth the price, especially with the amount of food. 2 nights there was just too much food for me.