Best way to send Javscript code with own Android app.

Actually the easiest way is to use free coding tool DroidScript with the free Puck.js plugin.
Here is the code (taken from the Puck.js plugin docs)

app.LoadPlugin( "PuckJS" );

function OnStart()
{
  lay = app.CreateLayout( "Linear", "VCenter,FillXY" );

  var code = "digitalWrite( LED1, 1 )"; 

  txt = app.CreateTextEdit( code, 0.9, 0.8, "MultiLine" );
  lay.AddChild( txt );
  app.AddLayout( lay );

  layHoriz = app.CreateLayout( "Linear", "Horizontal" );
  lay.AddChild( layHoriz );

  btnSend = app.CreateButton( "Send", 0.3, 0.1 );
  btnSend.SetOnTouch( btnSend_OnTouch );
  layHoriz.AddChild( btnSend );

  btnSave = app.CreateButton( "Save", 0.3, 0.1 );
  btnSave.SetOnTouch( btnSave_OnTouch );
  layHoriz.AddChild( btnSave );

  btnReset = app.CreateButton( "Reset", 0.3, 0.1 );
  btnReset.SetOnTouch( btnReset_OnTouch );
  layHoriz.AddChild( btnReset );

  microbit = app.CreatePuckJS();
  microbit.Scan( "Puck" );
}

function btnSend_OnTouch()
{
  microbit.SendCode( txt.GetText() );
}

function btnSave_OnTouch()
{
  microbit.Save();
}

function btnReset_OnTouch()
{
  microbit.Reset();
}