I'm pretty sure you'll need to be there to check the bags, since you'll want to do 3 bags on each ticket and (in theory) both of you should therefore be asked for photo ID.

I can't remember if there is curbside checkin at T4, which I think would be the only option to take the bags directly out of the car and for you to check them all in immediately.

If that doesn't work, I think your best option might be to have a skycap collect the bags, and then your mom can wait in the SkyPriority check-in area with the bags until you return, which will be 20-30 minutes. (There is a separate seating area there.)

Another option (if your mom is mobile enough to walk moderate distances but not carry bags, and if your bags are small enough to fit on a single smart cart) would be to return the car first, pile the bags on the cart, then you push the cart onto the airtrain from the car rental return. I probably wouldn't try this unless every other option failed, though. An alternative might be for you to drop off 3 bags with your mom (who can then check them in and get a boarding pass) while you take the other 3 with you when you return the car.