I know the cruise ship issue bothers some people - especially those who don't like crowds. I have stayed with a dive club at Eden Beach 5 times in the last 2.5 years, the most recent being last month. The day that the cruise ship is in port, there are taxi's that bring passengers to Eden Beach for a "day at the beach", and the parking lot can get congested with passengers, along with the open bar (used to be Bongo's) and the nearby beach. Not a lot more crowded than I've seen Buddies on a normal day. You can drive into the old Bongo's parking lot, walk thru the gate and you are 20-ft from the tanks. Probably closer than you can get when no cruise ship is there. I've seen "traffic" backed up for 20 minutes waiting to get air at Buddies Drive-Thru. I really don't think the cruise ship affects Eden Beach significantly enough for to rule them out on that alone.
Cody, I always try to do my own planning, because I can put together packages customized to my liking. That said, I tried to do that last January, when a buddy and I dove Bonaire. We wanted to do is inexpensively...it was all about diving, not beaches, bars, or fancy restaurants. I did a lot of checking around, and when all was said and done, no one could match Golden Reef Inns prices for what they offered. The excellent Wannadive dive op, car rental, and a nice functional (but not ritzy) one bedroom apartment package deal. The only thing Liz didn't package was the airfare, and she has helped me find deals on that too.
I'd be reluctant to recommend arriving on island and trying to sort out car rentals. I've been at the rental window when several without reservations were asked to stand aside while they helped those of us who had rentals (arranged as part of the package). I also heard the amounts quoted, and it wasn't the same deal as what you could get with reservations, when they had trucks available. Sometimes they asked the people to come back later, after trucks from a later departure flight were returned and cleaned. I think you can always get a week scuba package (weights and air) without prior commitment, but I'm not sure they will throw in the free Nitrox. Nor am I sure that they will match the prices that you can get with a package deal. But, as I said above, you can customize your package, I'd just do it all before arriving on island so I can get to diving immediately.