Like all other decisions, it depends on what your team needs.
Krookdile is faster, so can set up better. But it is slightly less bulky, and has lesser options to set up.
Incineroar is slow, but learns moves like swords dance to boost the move.
Overall, I'd say use incineroar, unless you have a baton passer (like ninjask with speed boost and swords dance and stuff). Then go for krookdile.