Weather
I tend to go the same time of year as you are considering. Weather is probably partly cloudy, highs around 90 and lows in the very upper 70s. At this time of year, you might get some wind reversals or flat calm days (tradewinds from the east are more typical). I also start to see some deeper thermoclines at the later part of your time window. Water is probably 82 to 80, even at depth.
Packages
Personally, I am not a huge fan of packages and often put together my own trips (to Bonaire and elsewhere). That said, Caradonna can do a nice package with air that might save you some $$. I would at least check in with them.
Most lodgings either run their own dive op or they have a relationship with one. I would tend to use wherever I am staying. For renting a car, I would get a truck (Telerin or AB would be my choices)
So, what might that all look like?
Lets do a one week package for two people. I will use room #1 at the place I stay at -- a one bedroom unit with a kitchen/dining area near the pool. The rate is $129/night. Tax is $5.50 per person per night. That makes the room $140 x 7 nights = $980. Then do 6 days of unlimited shore diving -- two x $99 plus 5% tax = $208. Add a pick up truck rental (Group 01) - $275/week all-in ($144 per week plus local fee ($5), second driver ($10), CDW ($77) plus taxes (5% plus $3.50 per day)). That is $732 per person. A single tank boat dive would add $20 per person per dive to the total. The only things missing are: airfare, food, gas, marine park fee and departure tax. And it is air and not Nitrox. All other taxes are included.
If you added a third diver, the room price would go up by about $100 (incuding tax), diving would go up by $104 and the price per person drops to about $556.
Lodging
Tons of solid choices. You will hear a lot about Buddy -- they do a nice job and they are the largest on the island so they tend to have the most visitors. IMHO, there are better options (based on my criteria) but for some Buddy will best fit their needs.
Can you give us some idea of your budget and what it needs to include? And how many in your group?
Here are the things to think about:
a) On the water or not?
b) Shore or boat diving or a mix?
c) How important (if at all) is Nitrox to you?
d) Big or small?
e) Kitchen or not?
Imagine the spot that you would like to stay at. Walk around that place. Spend an imaginary day and night there. As you reflect back, what seemed important to you?
a) By Bonaire standards, is it big or small?
b) Were there bars and restaurants? How far away? 24 hour front desk? Weight room? Shuffle board?
c) How important were room furnishings? Dishes?
d) Was town and/or other restaurants or bars close by to the resort?
e) Pool?
f) Location compared to other dive sites?
g) Prices?
h) What else did you imagine?
Do the same for the dive op:
a) What is the house reef like (do they have one)?
b) When do they do the diver orientations compared to when you arrive?
c) What should their boats be like (large, small, etc.)?
d) What is their shop like (rentals, repair, selections, etc.)?
e) Do they pump nitrox?
f) Where do you store your gear? How close is that to the boat? How close is that to parking? How close is that to the house reef entry/exit?
g) Instruction?
h) Prices?
Suggested next steps:
a) Start with the hotel list on Info Bonaire
Info Bonaire - The Bonaire Information Site - The Most Current and Up-To-Date Information Filter the list down based on pool, waterfront and price or size.
b) Then start looking at hotel web pages.
c) Then do a search on Bonairetalk
Bonaire Talk - The place to discuss everything and anything about Bonaire! .
d) Then post specific questions
My Preference
I tend to stay at the Carib Inn (10 plus visits).
Bruce Bowker's Carib Inn, Bonaire, Netherlands Antilles - Scuba Diving and Accommodations - Home Page
For me, the Carib Inn is great. I love the location. Most of the staff (including housekeeping) have been there for many years. The place is kept clean and well maintained. The gazebo is a great place to watch the green flash. The house reef is very good and the dive op and shop great. It has a pool and the dive gear is readily stored. The value is great (a room at the local Holiday Inn Express was going to be $171 plus tax -- at the CI that gets me a 2 bdr, 1.5 bath, kitchen/living/dining plus porch that opens one side to the ocean and the other to the pool) and I enjoy the staff.
Because it is small, it tends to be quiet. It is friendly. Because it is small, everything is close -- it is probably a 30 second walk from any room to the pool. It is probably a 60 second walk from any room to the dock. It is probably a 60 second walk from any room to the parking lot.
I stayed at a great place years ago that was not on the water and found I did one or two dives a day rather than three or four. For me, being on the water is worth it. Others might be more disciplined than I am...
Some might complain that the office is not staffed 24 hours or that there is no on-site bar or restaurant (both are a short walk away). Or that the bed linens are not 400 count. Or that small means there are not tons of new people you could meet every day. Or that they don't pump nitrox. For me, these are not issues...