AA and LY have an interline agreement so when she checks in at TLV she should ask that her bags be tagged all the way to SFO. She'll have to claim her bags and clears customs, then she'll have two choices: hand off her bags to LY and have JFK make the transfer to AA or take the bags herself from LY to AA and utilize a bag drop at the AA terminal. Either way, since the bags will already be tagged, she shouldn't be charged an domestic bag fee.

If for some reason LY won't/can't tag the bag, she can certainly explain that she is on an int'l itinerary and shouldn't be charged the domestic bag fee - and most agents will not charge it.

FWIW, I usually transfer my bags from terminal to terminal myself in order to limit the potential for lost luggage.