A Native Alaskan Co. doing work at an Air Force Base. No bond. If they are exempt from Miller Act is there security?

Your best payment security in that situation is your contract, along with being diligent in determining that the entity in question is reputable. 

I would also contemplate getting a personal guaranty from the actual person or persons you are contracting with. 

Aside from these items, it does not seem there are any laws that would assist you in getting paid in the event of non-payment by the entity.