The major bike store is in the Old City at HaHalutz/Smilansky; new & used bikes.
Aluf Sport Bike Shop at the BIG 08-6654726
TREK has a factory store on Derech Hevron (industrial zone/flour mill) 1-599-500-689, 08-623-7988
Schuna Bet: Off of Bialik near the produce market. Has small selection new and used bikes. Great service, very friendly.
Schuna Dalet: In Merkaz HaNegev off Metsada St. (behind Bank Leumi)