This is less an either/or than it sounds — a lot of travelers end up combining both. But if you’re choosing where to put your time and budget, the trade-offs are real.
The boat is both transport and hotel for the Luxor–Aswan stretch, which is the single most logistically fiddly part of an independent Egypt trip — no arranging drivers between Edfu, Kom Ombo, and Aswan, no packing and unpacking at three hotels. Meals, guided excursions, and onboard entertainment are typically included, which simplifies planning considerably.
Control. You choose exactly how long to spend at each site — useful if you want three unhurried hours at Karnak rather than a scheduled ninety minutes with a group. It’s also usually cheaper if you’re comfortable arranging your own drivers and hotels, and it lets you add stops (Abydos, Esna) that most standard cruise itineraries skip.
The boat solves the Luxor–Aswan stretch’s logistics in one move — that’s the real value, more than the cruise experience itself.
Many experienced Egypt travelers do Cairo independently (where drivers are cheap and easy to arrange), then take a Nile cruise specifically for the Luxor–Aswan leg, then go independent again for the Red Sea. This gets the cruise’s logistical benefit without committing the whole trip to a fixed schedule.
First-time visitors and anyone who dislikes trip-planning logistics: lean cruise. Repeat visitors, tighter budgets, or travelers who want to set their own pace at each site: lean independent, at least for the Nile Valley stretch.