两个说法都对（省略后面一个 by 的表达不如使用两个 by 的用法更正式）：

Shall we go by bus or train?

Shall we go by bus or by train?

我们坐公共汽车去还是坐火车去?

又如：

You can freight your belongings by air or (by) sea. 你可把东西经空运或海运运去。

One can travel there by ship or (by) plane. Most people choose the latter. 乘船或乘飞机去均可，人们多取后者。

Whether we go by bus or (by) train, it’ll take at least six hours. 不管我们是乘公共汽车还是坐火车，至少得花六小时。