A John Cowan was was one of those involved in the seige of Londonderry as part of the defense and his name appears in a document promising resistance to the Irish army March 21,1688-9. (Hanna, "The Scotch-Irish", Vol. 1, page 612.
A John Cowen of St.Johnstown,Gentleman, (?Derry) appears to have be a supporter of James I on the other side (P.611)
Whether these are related to your Cowans I can't tell.