The main sights are spread enough that some transit is useful. The Minato Mirai Line runs from Yokohama Station through Minato Mirai, Chinatown (Motomachi-Chukagai station), and on to Motomachi and Yamate, making it easy to string the highlights together without backtracking. Day passes for the line are good value if you plan to ride it several times.
Yokohama Station itself is a major hub with JR, Tokyu, Keikyu, and subway lines converging. The Blue Line subway connects Yokohama Station to Shin-Yokohama (for the Ramen Museum and shinkansen) in around 15 minutes. Between the waterfront attractions, the area is very walkable — Chinatown to Yamashita Park to Motomachi is all on foot.
Taxis are plentiful and metered. An IC card (Suica or Pasmo) covers all trains and most buses.