Traditional Hotels in Tokyo?

Can you guys recommend me any nice and affordable hotels in Tokyo Japan?
Or at least any affordable hotels that would be good for a honey moon? thanks

By "tradition hotel" do you mean traditional inn ie. ryokan?
http://www.japan-guide.com/e/e2029.html

Or do you mean standard western style hotel?

How much is "affordable"? (preferably in yen per night)

And for honeymoon do you want large rooms/nice bathrooms, or are you happy with a small room and capsule style bathroom?

What dates are you travelling?

This page is useful in explaining areas of Tokyo and offering some suggestions:-
http://www.japan-guide.com/hotels/tokyo.html

Let's start by suggesting Hotel Sunroute Plaza Shinjuku and work our way from there!
http://www.hotelsunrouteplazashinjuku.jp/en/

Enjoy your honeymoon!

If you want Ryokan, I can recommend to search in Hakone, Izu, Kamakura or Nikko.
Because in Tokyo, there are no affordable Ryokan for honey moon.
Now yen is too strong, and price jump extremely in cherry blossoms season.
So as GC3 said, you may want to show what you want and your budget.