It depends. To clarify, are you a bona fide resident of Puerto Rico or are you a US citizen that worked in Puerto Rico? According to this IRS source, if you are a US Citizen and not a bona fide resident of Puerto Rico, you must report your worldwide income. This means you will report your Puerto Rico income.
The good news is that you may receive a foreign tax credit for ALL taxes paid to Puerto Rico. In fact, according to this IRS document, all qualified taxes paid to U.S. possessions are considered foreign taxes. For this purpose, U.S. possessions include Puerto Rico, the U.S. Virgin Islands, Guam, the Northern Mariana Islands and America Samoa. This includes Social Security and Medicare taxes.
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