Mornings are generally better for 'local' conditions before the trades ramp up. Having said that the larger waves come from a long ways away and that is unpredictable.
There are locally-generated wind waves, and "swell" waves that propagate in from winds that are far away.
The latter arrive and don't care about local winds or morning or afternoon, and they can be problematic because their crest-to-crest (horizontal "length" of the waves) distance is usually greater than that of the locally-generated waves. The longer crest length means that the waves "reach down further" into the water column, and so provide more current/curge at depth, and stir of the bottom more. They may not be very high waves, but they have a lot of negative effect on the diving. Watching the wave crest arrive, count the seconds between them; more seconds means longer waves. 8 seconds and longer tend to be swell. the swell also arrives in groups, that is, a small wave, a larger one, the biggest one, then a smaller one, then the smallest one, then a calm period before the next group. You want to enter the water in the calm between the groups. Watch the waves for a while, and decide when to go in.
The locally-generated wind waves are a different animal. they are shorter-crested, often 5 seconds or shorter between crests, do not come in groups, and there is rarely a lull. They are harder to plan against. The trades winds (from East to West, so the west side of Bonaire is the lee side) don't vary much with the time of day. But time-of-day is important for the "sea breezes," which occur in the afternoon when the land gets hot and there is convection (rising wind currents) over the land. This pulls the nearby winds into the shore, thus causing shore-ward waves. If you are toward the southern end of the island, you get the trades sweeping across the flat topography and generating waves starting from shore and growing as you go offshore (with increasing 'fetch," as the sailors say). The seabreeze can counter-act that, and overwhelm it.
So, yes, mornings are typically better, because you don't get sea-breezes, not because the trade winds care.
WindGuru is not bad for the tradewinds/storm winds, but it ignores sea-breezes.