Is the frame of a glock considered the "firearm"? Meaning, must the exchange go through an ffl and in states which require, must the individual have a pistol purchase permit to accept the new frame?

the frame is the "gun" on a glock.  ffl rules apply

I had to get a frame replaced recently. As stated, the frame is the gun. And because of NJ's great gun laws, your firearm will have to be transferred back to you and you will need to use a pistol purchase permit.

Benefits of gun control. Preventing people from screwing up their brand new firearms

I have no idea on the NJ pistol permit, but yes the frame is the firearm. I had one replaced by Glock once and I had to pick it back up at an FFL, even though it was already mine, I sent it to them myself, etc.

I don't know about NJ laws pertaining specifically to pistol permits, but as far as having to transfer your gun:

The ATF says that if you are sending a firearm in for repair you don't need to transfer it again.

"Neither the transfer of a repaired firearm nor the transfer of a replacement firearm would be subject to the requirements of the Brady law. Furthermore, the regulations provide that a Form 4473 is not required to cover these transactions. However, the licensee’s permanent acquisition and disposition records should reflect the return of the firearm or the transfer of a replacement firearm.  [27 CFR 478.124-25]"

I have sent several Glock frames in for repair back to Georgia (back when the E-series 22s were replaced) with no transfers.  Call Glock and ask them and they should take care of you.