It is definitely personal preference. Generally a CAI is going to make a little more power than a SRI, at the cost of being slightly harder to install and clean the filter.
I have the MS CAI and sucking in water isn't really as big of a concern as people make it out to be. You'd have to drive through water probably 8-12" deep to suck in water. I've never had a situation where I've encountered water that deep.