Pure Boo takes it. Gotenks may be stronger, but he lacks the techniques to mitigate Boo's regeneration prior to his Rosat training and Boo's unpredictability and enhanced regeneration compared to the other Boos to the extent he was described as the most difficult to deal with makes it apparent how dangerous he is in a 1-on-1 fight.
Kid Boo takes this. Even with a strength advantage, I don't think Gotenks can completely disintegrate Boo to the point of destruction. That, and his lackadaisical attitude would surely lead to absorption, if not eventual death.
Gotenks is stronger, but the ki attacks displayed by pre RoSaT Goten and Trunks were pitiful in comparison to what's needed to destroy Boo. At best they'll be able to last until the end of their fusion, unless they get absorbed due to their own idiocy.