Assuming a 1 week first trip, and not knowing your experience but I take it your wife is a newbie, here's what I'd tentatively plan:
1.) Heading north, there's a point beyond which the road goes one way and you're committed to a long out-of-the-way trip around to get home. The 2 dives sites on that stretch I'd do one morning would be Tolo first, then Karpata.
2.) Before you get to that point, I'd hit Oil Slick Leap (plan to giant stride in) and 1,000 Steps (try to get a shot on the staircase with your wife; scenic & neat).
3.) As we move a bit southward, try Andrea I or II, or both. Pretty easy entry and generally good sites.
4.) A bit further south, but still a somewhat 'northern' or central site, The Cliff offers a small, shallow wall dive that's neat and different.
5.) Buddy Dive's house reef, headed north or south, is good. If you're good with gas, heading south you might reach Bari reef. Headed north, you hit the shallow boat wreck that's the south end of the Cliff dive site, and you pass Captain Don's Habitat.
6.) Harder for me to keep up with the order of the southern sites, so this won't be in order, but the Hilma Hooker is the big wreck dive that's one of the signature dives. And a nice reef (double reef system). Fairly deep dive for the wreck; figure to get around 80 - 90 feet as you loop around the far side, and you may see tarpon or barracuda. Alice in Wonderland is similar, minus the wreck.
7.) Angel City is a nice dive.
8.) Windsock - easy entry near that big wooden pier, which is a great marker for getting out if you night dive there.
9.) Salt Pier is popular. Seems people are always debating whether you're allowed to do it. Lot's of people do. If no ship is in, you could enter an adjacent dive site, such as Jennie's Glory or Salt City, and head down to it. Basically shallow diving around pilings, with schools of fish.
10.) Sweet Dreams is a far southern site with a very lush reef, kind of like Karapata.
11.) I enjoyed Red Beryl.
There are other good sites, too, but if you hit the ones I laid out, I think you can walk away from a Bonaire trip knowing you've hit a good showing of the main 'signature' sites. You could throw in Invisibles (long swim out, nice reef).
Richard.
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