Why do you need to choose now?
How soon is the cruise? Are there capacity issues? I very rarely do ship's shore excursions anyway, and never to somewhere I either know or can reach with ease on my own.
Or is this a case of you have "Free at Sea", so are using those credits? "Free at Sea" is one reason I would never sail with NCL as it is not really free.
Both of these can easily be done independently from Le Havre, if they do sell out, and massively cheaper. Rouen is an hour's train ride away, Honfleur a quick city bus ride.
Rouen is for the history.
Honfleur for the so French ambience, the attractive town centre, the markets, the boat trip under the Pont de Normandie and along the Seine. It has a certain "je ne sais quoi".
Given that my excursion next time I dock in Le Havre or Honfleur is Monet's garden at Giverny (done independently) that is a different answer. I too love both Rouen and Honfleur.
I've berthed in Rouen itself so many times, but there are still things I want to do there.
I understand your conflict. Very narrowly I would choose Rouen, but it's on the toss of a coin.
Have you been to Giverny, would it interest you? I assume NCL offer that option.