TL;DR: McCain did not invent that number (it does come from an economic analysis). But, it's complicated.
In 2015, the Government Development Bank of Puerto Rico commissioned a report (archived version) to assess Puerto Rico's economy. The report titled "Puerto Rico - A Way Forward" (by former IMF economists Anne Krueger, Ranjit Teja, and Andrew Wolfe) became known as the "Krueger Report" and it includes the following item:
Transport costs. All islands, remote from the centers of economic activity, suffer from high transportation costs. But Puerto Rico does so disproportionately, with import costs at least twice as high as in neighboring islands on account of the Jones Act, which forces all shipping to and from US ports to be conducted with US vessels and crews. Even those that consider the negative effects of the Jones Act to be exaggerated – e.g., outbound cargo rates are lower than inbound ones, as ships would rather not return empty – concede it is a clear net negative. Puerto Rico also has local laws that add to transportation costs – specifically, prices and licensing requirements set by the Public Service Commission for ground transportation.
Previous reports on the impact of the Jones Act have noted that it is not easy to tease out its effects from all the other factors affecting freight costs.
For example, a 2012 "Report on the competitiveness of Puerto Rico's economy", the New York Federal Reserve cited some representative numbers:
Available data show that shipping is more costly to Puerto Rico than to regional peers and that Puerto Rican ports have lagged other regional ports in activity in recent years. While causality from the Jones
Act has not been established, it stands to reason that the act is an important contributor insofar as it reduces competition (shipments between the Island and the U.S. mainland are handled by just four carriers). It costs an estimated $3,063 to ship a twenty-foot container of household and commercial goods from the East Coast of the United States to Puerto Rico; the same shipment costs $1,504 to nearby Santo Domingo (Dominican Republic) and $1,687 to Kingston (Jamaica)- destinations that are not subject to Jones Act restrictions.
However, this report also acknowledges that
While the Jones Act is often cited as a factor that raises business costs, there is no comprehensive, objective study assessing its potential effects on Puerto Rico’s shipping costs or the Island’s economy as a whole. Experts on the Island have varying views on the magnitude of the act’s effect, but most agree that the net effect is negative—largely because the act boosts the cost of imported goods to Island residents but also because it makes exports less competitive and diminishes the viability of the Island as a major regional trans-shipment port. However, some in the shipping industry argue that the net effect is minimal - that the restrictions effectively help establish incentives for more reliable
service and create jobs for American workers, many of whom are Puerto Ricans themselves, largely offsetting the adverse effects of higher costs.
Similarly, "Puerto Rico: Characteristics of the Island's Maritime Trade and Potential Effects of Modifying the Jones Act", a GAO report from 2013, concludes:
so many factors influence freight rates and product prices that the independent effect and associated economic costs of the Jones Act cannot be determined.
Also see: "Economic Impact of Jones Act on Puerto Rico's Economy", a report by two University of Puerto Rico economists presented to the GAO.