US CONGRESS is not above IAEA or NSG. It is similar to Indian Parliament. Today there is an internal US Law that does not allow a US President to sign an Agreement of this nature, it is called HYDE ACT.
123 Agreement stipulates that before it comes into affect, both countries will have to ratify it. India is a parliamentary system and thus does not require any ratification since ruling party has to have a majority. However, US Congress has to ratify it and to do so it will have to amend its own Hyde Act to allow US President to reach an Agreement with India by making it an exception.