Hi tigger12jb!
For our first cruise we wanted 4 days at the Polynesian and a 3 day cruise. When I went to book the land/sea package (several months in advance), the only deluxe resort they offered was the Dolphin. This led me to consider booking WDW and cruise separately, and it turned out to be a much better idea. Excellent discounts became available both for the cruise and the Polynesian, so that we stayed concierge at the Polynesian and category 5 on the cruise, both at great rates.
While those rates are hard to come by recently, booking separately gives you a lot of flexibility and is very likely to save you money. The only thing you really lose is the convenience of paying one price, and having a room card that works in both places, which means you don't need to go through the registration line at Port Canaveral with the package.