I usually just lurk on scubaboard, but since I recently had the same question, and being an engineer in real life, I investigated boats and web sites, put them in an excel spreadsheet, and made a nice chart upon which I could base a decision. If it helps you, here’s what I came up with.
I was looking for something in the Caribbean, I always dive nitrox, and I vastly prefer a 5-dive-per-day schedule, plus enough days of diving to make the travel cost-effective. (The Blackbeard's sailing vessels (Pirate Lady, Morning Star, Sea Explorer) do not have nitrox, so they don't make my consideration list, but I'd already added them to the spreadsheet before I figured out there was no nitrox, so they're in the chart.) In computing the total cost per dive, I included the extras for each charter (nitrox, fuel surcharge, port fees, park fees, beer/wine when not included – I like (just one) beer or wine after the night dive).
One other thing to consider is the amount of crowding. I don't need luxury, but I don't want every square inch of space covered with people, either. The right way to compute this is to determine the sq. ft. of usable space on each boat and divide by the number of passengers, but that was too retentive even for me, so you'll need to look at the web sites and make your own qualitative judgment.
Hope this helps –