MJZ-
Duane, Pete, and Brian have all gave you good info.. On a boat, I would purchase the dealer as much as the boat and how well they will take care of you during and after the sale. Finding good boat dealers is even harder than finding a good motorcycle dealer.
If you want a Whaler, your only prerigged engine choice is the Verado as both companies are owned by Brunswick. If you want a Zuki or Yammi, the boats are sold with no controls/gauges and a lot of dealer work is required which isn't cost effective. I also think Whalers aren't what they were before the bean counters at Brunswick took over.
I wouldn't be afraid of any of the O/B engine choices that are available today (even a 2stroke ETec).