应该是A
which作为疑问代词,指代前面的a boat,把a boat代入A和B：
In a boat they could get to the island.
By a boat they could get to the island.
By a boat 显然是错的,正确的应该是by boat=in a boat.
与此类似的还有
by car=in a car
by train=in a train
等等