Yes — if you're visiting in July or August and the midday crowds are a concern, the sunset slot is the most elegant solution. The Blue Lagoon's colour is the same at 5pm as at noon, but the floating pontoons and rocky shoreline are far less congested. Daytime traffic at the lagoon peaks between 11am and 3pm; by the time a late-afternoon departure arrives, the bulk of those boats have already left. What you get is the same famous turquoise water, the same limestone cliffs, the same swimming — but with room to breathe, and the added bonus of Comino lit gold as you sail home.
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The honest caveat: swim time is shorter than a full daytime cruise. Most sunset cruises allocate 45–90 minutes at the Blue Lagoon; a morning or full-day cruise gives 1.5–2.5 hours in the water, plus time at Crystal Lagoon and the sea caves. If swimming for two hours is the entire point of the trip, a daytime departure will serve you better. If the atmosphere, the light, and a quieter Blue Lagoon matter as much as the swim, the sunset option is hard to beat.