Go with Amigos del Mar, aside from being probably the premier operator on the island, they also have the best boat for the Blue Hole trip, a Pro 48.
There is no beer on the boats for the close in trips, cuz you are back at shore in just a few minutes. But they do have panty-rippers and Belikens for the return from the Blue Hole and Atoll day trips.
As for the best sites for seeing animals, well, ya just never know. I really enjoy Cypress, Pillar Corals and Boca Ciego. (last time I was at Cypress the place was crawling with nurse sharks swimming about freely) However, Victoria Tunnels are fun too . . . well, thing is ya just never know. Over the past few months on two separate trips, I saw different fish on different sites from the trip before and even the year before. As in most things, luck and timing are everything. I've never seen a reef or bullshark on any of the close-in dives; that doesn't mean that they are not there. Not too long ago while riding in a boat on the north side of the cut, but well inside the reef, I saw a bullshark.
I have seen many many sharks in the Blue Hole and on my second last time into the BH, was close enough to touch one that came to see me.
On the other hand, on my last time in the Hole, I saw only one shark and it was quite far away.
If you take Amigos to the Blue Hole, they divide up the groups of divers into one or two groups. Group One goes in first, gathers on the lip and descends, then group two follows, etc. Talk to the DM's well before reaching the Hole and before they make up the groups. Tell them that you want to be in the last group. That is the group that has the best chance for shark encounters.
(I should quit telling people this, or no one will ever want to go in the first group)