Yokohama is pretty big...... only the second largest city in Japan.
Ok top 3 major stores in central Yokohama and within walking distance of the station are:
Y's road (crap service, zero knowledge base, lots and lots of stuff especailly spares) = http://goo.gl/maps/InQN2
Bike Run (small shop may need to order parts for you but awesome service and he knows his stuff highly recommended, cheaper than Y's)= http://goo.gl/maps/ys8cb
MyX (mtb specific, they know thier MTB stuff and have a great mechanic) = http://goo.gl/maps/PF0dp
However, THE best store in Yokohama is Sagami Cycles (This is only 1 of 2 shops I will let touch my bikes) Great service, great mechanics, great prices, just great!: