Yes, this can be done but not from within the Make-Table query. You have to execute VBA code to create the additional field and the primary key. Try the following and change the names of the query, database, table, and field to your specific needs.
DoCmd.Setwarnings false
docmd.OpenQuery "qryMakeTable"
DoCmd.SetWarnings true
Dim db as DAO.Database
Set db = OpenDatabase("c:\FolderName\YourDatabase.mdb", True, False)
db.Execute "ALTER TABLE tblYourTable ADD COLUMN RecCounter AUTOINCREMENT"
db.Execute "CREATE INDEX RecCounter ON tblYourTable (RecCounter) WITH PRIMARY;"
Let me know if this works for you. I use it all of the time.
db.close Bob Scriver