I feel like of those three, Greninja is probably the most threatening to Bowser if I had to pick one. His good run speed and low profile allow him to always slip under Bowser when he's trying to land and Bowser's got some pretty poor landing options if the opponent is right underneath him as he's about to land. Bowser can Side B somebody if they just run up and hope to shield an attack, but with somebody that fast Bowser can't confidently predict which direction the Side B should be aiming and it's a very laggy move to miss, A spot dodge also beats any of Bowser's landing options until he starts reading that option. If Bowser feels too threatened to land, he'll retreat to a ledge, granting you stage control which is a big deal.
Greninja's got excellent edgeguard tools against Bowser. Hydro Pump really screws with Bowser's Up B, forcing a lowest possible trajectory, and Greninja can just D-air Bowser's Up B for a meteor kill at that point. Just remember to recover since Fortress often trades with that move, causing Greninja to fall rather than bounce off. Substitute can also send bowser in the direction away from the ledge if you can get in front of his Up B. Your gameplan should exclusively be focused on getting Bowser offstage for edgeguard attempts, because Greninja can't keep up with Bowser's damage and KO potential in a regular fight.