Cuba: Is it legal for Americans to travel to Cuba via Cruise Ship?

The answer is yes. Technically, Americans are still not allowed to freely travel to Cuba unless they meet one of 12 criteria with the two most common ones being mission trips and people to people cultural exchanges. The cruise lines sailing to Cuba from US ports have qualified to do so by meeting the people to people cultural exchange requirements.
As per NCL, who will be operating cruises with an overnight in Havana: A people to people exchange is defined as a traveler who maintains a full time schedule of educational exchange activities intended to enhance contact with the Cuban people and that will result in meaningful interaction between the travelers and the people of Cuba. The traveler must self certify that they have met these requirements, by keeping a log of their activities and impressions whether they explore on their own or through a shore excursion offered by NCL. The traveler must retain this log of activities for 5-years from the dates of travel. Travelers must fill out a form indicating they meet the people to people requirements as set forth by OFAC, they must have a valid US passport that does not expire less than 6-months from your last date of travel in Cuba and must obtain a Cuban visa. NCL can process this visa for a $75.00 fee.
I have visited Cuba and the advantage of visiting by ship, means consistency in the level of accommodation and ensures the traveler a place to stay. Cuba's infrastructure is struggling to meet the increased demand, and accommodation levels are not yet up to US traveler's expectations.
I would be happy to assist you in planning your Cuba cruise. But don't delay, as there is limited space and it is bound to sell out quickly.