Dork Fish:
I know what you mean about eyepopping from all the research. I tend to do that myself. But at some point you have to accept that you will have a great time and it isn't necessary to make the perfect plans and get the perfect price.
I second (third, tenth?) the rec for
Hotel Coz, AI style. On the southern edge of town, a 15 minute walk or $3 cab ride, Chedraui super mercado is two blocks north. I've found the adder for AI is only about $30/day per person (kids 12 and under stay free) and you can get your money's worth just from breakfast, snacks, and drinks even if you do eat out. We like to go into town a few times and have a few nice meals, but most of the time we just want to just eat something and get it over with. After a long day in the hot sun and saltwater, maybe with a sunburn or a buzz from poolside daquiris, we'd rather not have to spend 2 or 3 hours to catch a cab to town, make a decision on where to eat, deal with the crowds and the wait, and catch a cab back. It's nice to wander into the onsite restaurant, eat from the buffet line, and be out of there and back in the room or lounge chair in 30 minutes.
The prices you've found are not bad but should get better. They aren't discounting yet. The best deals are the last minute deals but you'll start seeing deals sometime in April/May. In your separate pricing, you left out the airport/hotel shuttles, which will be about $15/person RT to Hotel Coz but are included in total packages.
Some may disagree, but I've found the bottom line deals about the same (+- 5%) from the various vacation package operators, at any given time. The deals originate from the hotel although you won't get your best price directly from the hotel. They know the operators are their ticket to success and they want you to book through them.
Expedia will be competitive with anybody and is a well known name that will adhere to it's policies. Research the terms of those policies regarding cancellation procedures, etc. I wouldn't trust some company I've never heard of - anyone can throw up a nifty website. In reality, many of them are all owned by a few people anyway. For example, Expedia owns hotels.com and many others.
On the other hand, airlines offer their best deals on their own website. You might do better booking hotel through an Expedia-type operator and the airfare directly.
If you go with
Dive Paradise then upgrade to their faster boats. It's not much more and their cattle boat is s..l..o..w.. You'll have dive lockers by the dock next to showers and rinse tanks. Some ops will store your gear for you but I like to keep mine nearby in case I want to hop in for a shore dive or just check something out. You can also book hotel/dive packages with Dive Paradise.
I just checked Funjet for your dates, air/hotel/shuttle for $2820, add the $300 for diving and you got about $3120.