it's not bonk's adventure, not only was it on tg16, i dont remember any monkeys at all in that game.
droptheoxygen, is it Joe and Mac? you were a caveman (or 2 players were cavemen) that ran through the level fliging various weapons like bones, boomerangs, or fire at the dino enemies. They weren't monkey men though. I definitely remember a trex boss on the first level, though i don't think you fought inside one of the boss dinosaurs stomachs until a later boss. the level select style was that of mario 3 or mario world though, not like megaman.
perhaps this is not the game you're thinking of, though maybe it will help you remember.