Keep in mind, "best" is relative. There's lots of good operators in the Kona area, each is different, their boats are different. If a large boat with a working head is important to you, two of the companies mentioned so far have that. The OP mentioned he wanted a smaller less crowded operation, keep in mind every operator mentioned runs mostly boats holding 12 or more passengers, and during late June and the rest of the summer, those boats are likely to be going out at or near full capacity (hopefully anyway, all the operators are looking forward to the busy season). No 6 pack boats have been mentioned, some people would never try a 6 pack boat while others prefer them over larger companies, to each their own. If a diver's looking for a boat that'll carry a max of 6 passengers, and often has group sizes lower than that, take a look at a 6 pack boat.
At any rate, no matter what size of boat you're looking at, take a look at what they offer for diving if the diving end of things are important for you. How long are the dives? If you're good on air and can do a 90 minute dive, will they let you? What is the typical group to guide ratio? What's on board for eats? Boat size and bathroom facilities (if important to you)? Minimum group size, and what do they do if they come up short, will they cancel on you because there aren't enough other divers? How long has their dive crew been doing this? etc. Lots of variables can go into choosing what's best for you.
Just throwing it out there, there's lots of good options in Kona.