How do you count all the Agile boards I currently have in my JIRA instance?

Procedure
This can be done by directly running an SQL select query from the database:
SELECT COUNT(id) FROM ao_60db71_rapidview;
This will return the number of boards regardless of Kanban or Scrum.

Kanban Specific
To get the number of Kanban-only boards:
SELECT COUNT(id) FROM ao_60db71_rapidview WHERE SPRINTS_ENABLED = 0;

Scrum Specific
To get the number of Scrum-only boards:
SELECT COUNT(id) FROM ao_60db71_rapidview WHERE SPRINTS_ENABLED = 1;