I'd say either just Yahwism or both. For sure he would have praticed Judaism, but it doesn't neccessairly make you a Yahwist (one who has sincere faith). The distinction between Yahwism and Christianity is Yahwism is pre-Christ faith, whereas Christianity is not. It may be a matter of opinon whether or not Christianity began after the death of Jesus or as soon as He began His ministry. John the Baptist mainly talked even before Jesus began His ministry.
To be "official" I'd say he praticed Yahwism. With his case there is kind of a gray spot of what his religion officially was. In the end John the Baptist had faith so his religion would be one that follows and upholds God.