There are pros and cons to both,

I mean getting very technical then you can look at the Specific heat capacity(SHC) of air against water, for instance SHC of air is 1005-1030 J/kgK but water is 4187J/kgK this means that it takes about 4 times as much energy to change the temperature of water than it does air, so when the chargecooler gets hot it stays hot longer, but it also takes longer to get hot than an intercooler would, theoretcally anyway.
the other pros and cons would be the packaging issues like Mr. Rainbird suggested, in all fairness I would be inclined to follow suggestion and see if what you already have is coping.