Thanks so much for all of the helpful responses!
The hard part about the land/sea package is that you must get a verandah room on the cruise in order to get a deluxe hotel. And I don't even want a verandah since I will worry about my 3 year old getting out there (even though I will be watching him).
So, in case anyone is wondering, I priced out the separate booking with a stay at WL for four nights with the three-night cruise with a deluxe ocean view room and with park hopper tickets for four days for two adults and two kids and got a total of $3,376.
I then priced out the land and sea package with the four-night deluxe hotel (Poly, AKL or BC, for some reason WL was not an option?!) and the three night cruise with a verandah room (which I don't care about but must choose to get a deluxe hotel) and with ultimate hopper tickets and the total was $4537. I did not pick ground transfers, we will not need them as we will have a car.
So, based on our needs I think I will book separately. In doing so, I will still stay at the fabulous WL, I will still get an ocean view cabin, and having preschoolers I doubt I will need more than the park hopper tickets. Doing this will save us $761, a substantial amount!
Thanks again for the advice.