I picked Cyndaquil. Why? Well, quasi-long story. Totodile is definately my favorite of the HG/SS starters (if only because Feraligatr is badass), but there are a multitude of great water types around. Chikorita (and by association its evolved forms, Bayleef and Meganium) are nice and all, but their move sets are, well, boring. That and both of them are relatively slow without any real standout attacks. Cyndaquil, and by association Quilava and Typlosion, gets some interesting moves, both standard and TMs and is pretty quick and fire types aren't too easy to come by in the early game.
TL
R version - Cyndaquil and evolved forms are the best at high levels.