By what method do you propose for the President to declare ANTIFA a "Terrorist Organization"?
In the legal sense a "Terrorist Organization" refers to a designated "Foreign Terrorist Organizations" and are designated by the Secretary of State, not the President, under section 219 of the INA.
So, here's your first problem:
Legal Criteria for Designation under Section 219 of the INA as amended
It must be a foreign organization.
Take of look at the official State Department list here:
https://www.state.gov/foreign-terrorist-organizations/Notice, there are no U.S centric organizations on the list.
Although the FBI will discuss groups as "Domestic Terrorist Threats", or "extremest groups". However, Generally, there groups engage in much activity that is protected by constitutional guarantees of free speech and assembly, so there's no constitutionally permissible equivalent designation for groups engaged in domestic terrorist activity.