EWR is not, technically, a part of the NYC city code, so there is a separate set of AA fares:
[KVS Availability Tool 2.9.2/Platinum - Sabre: Fares/ZUJ/SG/USD]
Code:
EWR New York Newark Liberty Int'l NJ US [KEWR]
SAN San Diego Metro / San Diego Lindberg Fld S Diego CA US = CLD SAN [KSAN]
RT Oct-Sep
Carrier From To Fare Cur Expiry Min Max Fare Basis
--------- ------ ---- --------- ---- --------- ---- ---- ----------
AA EWR SAN 279 USD 12 Dec Q143SQPN
AA EWR SAN 297 USD N14E3PN
AA EWR SAN 335 USD S14E3PN
AA EWR SAN 391 USD G14E3PN
AA EWR SAN 447 USD V10E3PN
AA EWR SAN 503 USD W10E3PN
AA EWR SAN 559 USD W7E3PN
AA EWR SAN 652 USD L7E3PN
AA EWR SAN 689 USD M3E3PN
AA EWR SAN 745 USD KA3Z
AA EWR SAN 1119 USD H26
AA EWR SAN 1193 USD KUPPMZ
AA EWR SAN 1296 USD Y26
AA EWR SAN 1381 USD YUPMZ
AA EWR SAN 2207 USD F26
AA EWR SAN 2988 USD Y
AA EWR SAN 3646 USD J
AA EWR SAN 4584 USD F