This will depend on whether EB1A/NIW is mentioned specifically in the recommendation letter. For example, if the recommendation letter has the sentence “to support Dr. XXX to apply for a green card as an alien worker with extraordinary ability”, you might not want to use it in your NIW petition. If you want to apply through both EB1A and NIW at the same time, you might want to prepare a set of two recommendation letters (one for EB1A and one for NIW) for each referee. The difference between the two letters could be just one sentence.