Rather than the Yaesu Fujiya, I'd opt for the Hotel Metropolitan Marunouchi or the Marunouchi Hotel:

http://www.jrhotelgroup.com/eng/hotel/eng155.htm
http://www.marunouchi-hotel.co.jp/english/index.html

The latter is likely to be a little more expensive, but both are newer and closer to the station than the Yaesu Fujiya.

The Yaesu Fujiya may be a five minute walk from the Yaesu side of the station (not the same side as the N'EX), but it's not pleasant to schlep across the six-lane Yaesu Dori with luggage in tow. As recently as last year, the hotel itself was decent but "old" with reproduction Louis XIV chairs, chipped paint and faded carpets. Tripadvisor may give you a more recent perspective.