Two independent water cooled units are probably 'best' for a larger boat. With the boating industry essentially prostrate during the current depression .... very good deals can be readily negotiated for major items.
Air-cooled AC units will be about as equally popular as a wind-howling roller furling mast by your slip mates.
Strictly water cooled ACs have the best efficiency (power consumption, size, variability of control (heat/cool/dehumidify, etc.) ... the newer modern and efficient draining 'drip pans' from some manufacturers have eliminated the 'super-stinkey mold/mildew factories'. Most newer designs are smaller, lighter weight than previously.
Many of the newer units will soon ship and use the newer "green" refrigerants - as the Montreal Protocol for the 2010 moratorium of most freons is now very quickly approaching ... you will have to decide/bet on buying an AC that if needs a 'recharge' in the near future if the remaining 'freon' stockpile will then be 'still available' .... or NOT.