plt=Graphics3D[{Sphere[{0, 0, 0}, 1], Sphere[{2, 3, 5}, 1]}];
    Append[plt, Boxed -> False]


Edit1: 

 If we have use
    
     plt=Graphics3D[{Sphere[{0, 0, 0}, 1], Sphere[{2, 3, 5}, 1]}, Boxed->True]
 
 the above codes fails.
 To make them more general, we can use:

 

     Append[DeleteCases[plt, Boxed -> _], Boxed -> False]