Both kinds of cruise cover the exact same water around Comino — a swim stop at the Blue Lagoon, a cruise through Crystal Lagoon and the Santa Maria sea caves — so you're not choosing a better or worse lagoon experience. The only thing that changes is Gozo. A Comino-only cruise is the shorter, cheaper, swim-focused day; a full-day Gozo and Comino tour bolts on 2–4 hours ashore on Malta's quieter sister island, with the hilltop Citadel in Victoria or the red sand of Ramla Bay.
So the decision is simple: if you mainly want to swim, snorkel and relax on the water, book Comino-only and keep the day short and inexpensive. If you'd like history, food and a different island on top of the lagoon, the full-day Gozo tour is the most-booked option in Malta for a reason. Just know that a day trip gives Gozo only a few hours — enough for one highlight, not the whole island. Below is the side-by-side, and the best-rated pick for each.