If the income on the 499-R and the W-2 is the same income but reported on both forms you do not enter the 499-R on the U.S Form 1040. Doing that you would be doubling the amount of income.
If you are a Bona Fide resident of Puerto Rico per the Bona Fide Residence Test you can exclude income under the Foreign Earned Income Exclusion provision in the tax law.
If you are not a Bona Fide resident of Puerto Rico you can take the Foreign Tax Credit.
Also see this article. Posting a 499r.
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