At what stage should one when say ’Hamapil’ before bed.? When he is already undressed in his bed clothes or before he gets undressed and into bed?

There is a dispute among the poskim if Hamapil should be said before Shema or just before going to sleep. However, all agree it should be as close as possible. The Mishna Brura (Orach Chaim 239) says that if one is concerned he may fall asleep before saying Hamapil, it should be said before Shema and if one is not concerned it may be said afterwards. Just before sleep most people would be in their pajamas. So as long as your remain modest with your bedclothes you may recite Kriyat Shema Al hamita in bedclothes.