Stopping in Hamburg on a cruise. Would should I not miss

See the harbor and take the Port Guided Boat Tour, though you'd be leaving one boat and getting on another. The St. Pauli Landungsbrücken Harborfront is an atmospheric people zone with boardwalk ambience. See the famous Reeperbahn red-light and nightlife district, where the Beatles got their start in the 1950s/60s. The International Maritime Museum is excellent. The St. Nikolai Memorial is a bombed-out church memorializing the destruction of World War II with excellent museum and view from its tower. There are other sites, but I found the atmosphere of Hamburg to be quite captivating. I prefer it to Munich and consider Hamburg the equal to Berlin in atmosphere.

Speicherstadt
Emigration Museum
International Maritime Museum
A coffee roastery

This place:
https://www.miniatur-wunderland.com/
It's Hamburg's post popular attraction and right up there with the Taj Mahal, and Sistine Chapel, as one of the greatest wonders of the world.

The Neuengammen camp site is located in Bergedorf , to which you can access by taking the S-Bahn from Hamburg Hbf. British troops got to it in early May.

You do have time to do a harbour cruise. Arrange that in Landungsbrücken, where your drop-off point is at 8 AM.

The first question actually is which of the three possible cruise docks in Hamburg you are using. Do you know?

I agree with Michael. Go to Minatur Wunderland.

It's the main reason I visited Hamburg a few years ago. I plan to go back in a couple of years when they have finished the newer exhibits.

If these two things are must-dos, I would make sure to take a few minutes to visit the Krameramtstuben--or at least the alleyway--just behind the Michel (St. Michaelis).

Is there a particular reason for wanting to see Neuengamme? Have you ever been to a KZ or would this be your first camp?

Others have mentioned the harbour tour at Landungsbrücken. I would put a caveat on that and say it depends on your timeframe and your interests. I do wholeheartedly second Rick's recommendation of the Maritime Circle Line Tour. But from the Landungsbrücken, you can walk up the Portuguese Quarter to the Michel and from there you can walk down to the St. Nikolai church. This is a bombed out footprint of the church with only the gothic spire left. Then cross back across the main road (Willy-Brandt-Straße) to the Deichstraße, a street that has mostly survived Hamburg's many destructive events. Duck in between the houses and onto the pontoon and view the street from the canal side. Cross the next big road and the water to the MiniaturWunderland and Speicherstadt. You don't have to go into MW--though it is CERTAINLY worth seeing!--but could instead walk down to the Elphi, the giant philharmonic. It's free to go up to the viewing deck, and I recommend doing this! From there you can get a ferry back to the Landungsbrücken. Then you could head straight up the hill and you would be on the Reeperbahn. Or walk along the water down to the Fischmarkt (square and Fischauktionshalle). If you do that route you could pop across the street and look briefly at the quirky park (behind Überquell). That's a generic walking tour that can get you a lot of highlights in a short time.

More knowledge of your interests and cruise terminal can help us tailor our advice.

As stated above it is not possible to give accurate advice without knowing the terminal you are using and the day of the week you are visiting.
Many of the bigger ships are now using Steinwerder terminal. There is a water bus/ferry from there only on Monday to Friday. At a weekend it is either ship shuttle bus or public bus/S Bahn into the city (or a 30 to 40 minute walk there via the under river foot tunnel) into the city.
Apart from Landungsbrucken the other terminal is at Altona which has a ferry to Landungsbrucken 17 hours a day, 7 days a week.