Given that fact that Kid Buu needed to be hit with a massive spirit bombed, assisted by SSJ [maybe SSJ2] Goku; I don't think Gotenks has enough in the tank to end Super Buu.
I will admit that Gotenks did appear noticeably superior to Super Buu.
-edit-
I just found the chapter in which he fought Gotenks. Goku looked very sure he could kill Super Buu after Gotenks' fusion wore off inside him. Super Buu also looked very sure he was going to die, as well. This was actually Super Buu + Piccolo. Gotenks could actually win. I really don't know, now. It's a toss up.