I think "bumpy" works fine in the context. The sea was rough, but "rough" has other meanings when it comes to accommodation and holidays in general, so there is a mild risk of it being misunderstood. If you changed the sentence to make it clear that you are referring particularly to the sailing, then "rough" is fine: "We had a rough passage to Le Havre", for example.
Turbulence in the air can feel like going over bumps in the road. Since you don't have that on a cruise, I'd take it metaphorically and assume that there were lots of minor problems (the buffet ran out of shrimp) rather than the seas were choppy.