Pinyon nuts can easily be obtained at the Followers safehouse when Doctor Luria is there. While she is there, each time a refrigerator is opened, it will immediately spawn up to three new foods, replacing any previous contents. The spawn list contains only 23 possible foods, of which pinyon nuts are one.
East pump station: one on the right as you enter, on a bench in front of some lockers. One on the left, on a table next to two boxes of Potato Crisps.
Found on the bedside table in the El Rey Motel, in the 2nd room on the second floor of the motel, where the dead wastelander is. There are more pinyon nuts on the bedside table of the motel room on the first floor (the only room that is accessible), where the bark scorpions are.