Yes, chinchin is indeed Japanese for penis. It doesn't really (or at least necessarily) mean a small one, it's just a vaguely cute diminutive form often used by women, especially mothers to children. The closest English analogy would probably be weewee. Quite often the honorific o will be tacked on, resulting in o-chinchin, "honorable weewee".

The original version is chinpo, which is quite rude. This is, incidentally, also the word spoofed by the legendary Chinpokomon episode of South Park.