So I got the lucky 38 penthouse and i'm there now with boon, but i want to know if there is a way to make him wait there with out him just standing there. Like in Skyrim if you dismise a house carl they would wait at their house, but if i dimise boon will he go back to the dinosaur?

You will have the option of sending him back to Novac or to the Lucky 38 if you dismiss him.