One of the most logical ways to relax US trade restrictions with Cuba without unnecessarily injuring the fragile Puerto Rican economy would be to require imports and exports between Cuba and the US to be cleared through, inspected by and accounted for through Puerto Rican ports - either in San Juan or Ponce.
Since Puerto Rico is a US territory and not a state, it would seem perfectly rational to "legalize" or relax trade between Cuba and this US territory without fully legalizing direct trade between Cuba and the US.
Puerto Rico's finances will be hugely impacted by the US opening up trade with Cuba. Making Puerto Rico the port of entry and exit for trade goods (such as cigars) shipped between Cuba and the US would benefit Puerto Rico's economy and would be an easy policy to implement.