The best choice would probably be Totodile. I'm not saying that because I love all water starters, but mainly because it doesn't have any weaknesses against gym leaders in johto and it learns ice fang which can give you an advantage against Claire and Lance. In kanto it only has two weaknesses, Lt. Surge and Ericka. Also Feraligatr is kinda powerful too.
Cyndaquil is good but Whitney would give you a rough time with rollout and Claire will give you a rough time with Kingdra and Gyarados as well. Lance's gyarados is powerful too . In Kanto, it will be weak against Brock, Misty, and Gary's Rhydon and Gyarados is very powerful also.
Chikorita is weak but has good defense and will probably have the hardest time beating the game with it.