The Kujukushima cruise that I took didn't stop off on any of the islands. The scenery is very nice, but I suppose it's best done on a sunny day. It takes off from the Pearl Sea Resort, which has shops, restaurants, an aquarium that I thought was worthwhile with a nice dolphin show. There's an area where you can pluck a pearl out of the oyster shell yourself, but I did not try that. I believe you can also do things like kayaking.

Huis ten Bosch (I had the spelling wrong), to me, is pretty amazing. It's a replica of a Dutch town. It seems like people either love or hate this place. I personally love it, and I think it's really nicely done. Even though some people think it's phony, this type of theme park is only-in-Jpn type of experience. I'm not sure that you'll be impressed with their museums or rides/attractions. But it just has a very nice ambiance with windmill, gardens, canals. They have boat rides around the complex, and you can rent a bike to roam around on (which I'd recommend). There's laser / light projection mapping show at night, which was impressive.

Biopark is at: http://www.biopark.co.jp/en
Lots of hands-on opportunities with the animals.

I think you'll have to research these places and decide for yourself which is your type of place. Personally, I'd choose HTB, but it may not be a safe recommendation since I'm afraid some Western visitors might be put off by that type of attraction in Jpn. The Shimabara/Unzen option may be a good one to consider, and one that perhaps most everyone can agree is very nice for all visitors to Nagasaki. Hopefully, other folks will chime in with their 2-cents.