It really depends on the situation if my assumption of how it works is true. I assume the buff is based on percentage so you would want to hit/boost the higher number. Lets say the base numbers on either side are 55,000 defending and 50,000 attacking and the hit/boost is 10%. In that case, since your base points are higher you would want to boost your def 10% or 5500pts instead of hitting your attacker 10% which would only be -5000pts from him. However, if the numbers where reversed with your attacker having the high base number you would want to hit their attack not boost your own defense.
With that being said I would say the majority of players have a higher attack deck than defensive deck, therefore I think an attack hit skill would be better.