The answer is sometimes. If a wisdom tooth has a deep cavity and has a pulpal exposure it can be a good candidate for endodontic therapy if it has errupted in a cleanable position and is in good function. Like other posterior teeth, after having a root canal wisdom teeth should be crowned. In my practice I recommend full metal crowns for wisdom teeth(and second molars), since the chewing pressure they can experience can make porcelain breakage more likely when porcelain fused to metal is used.
If the wisdom tooth is not fully erupted or difficult for the patient to clean, then root canal is not the best option for dealing with a compromised pulp. Instead extraction is the best option. In this event, often the opposing wisdom tooth is extracted as well, since without an opposing tooth present, it may extrude over time.