I also have both. I have heard the bunnies drink more water from a crock which helps keep calcium levels down. (and this is especially important for bunnies who seem to have an inherited issue with calcium buildup)
I think both can have positives and negatives.
My opinion on crocks:
Positive: Drinks more water. Quick and easy to clean
Negatives: Even with heavy crocks that don't get tipped over, bunnies have a talent for getting all kinds of things in them, like hay and poop, and even part of a blanket that will soak up the water.
Positive: Good for insuring enough water is available at all times. Keeps water free of debris.
Negative: Harder to clean. Can clog, and seal wears out over time. Noisy if nearby during human sleeping time!
And bacteria can actually grow in either. It's all about cleanliness. I think the reason that bacteria may be thought to grow in water bottles vs crocks, is because water bottles can be harder to clean out. Some suggest to clean water bottles daily. But I think most people change it when it gets low, after a couple of days or so. (depends on how much greens are incorporated into the diet - they are higher in water content) . I mean I think that is how they were meant to be used. So I do not know really if harmful bacteria grows in just a few days. (another thing for me to double check on, and if anyone else knows facts about this - please share)
But if the water bottle sits there for days on end because a bunny gets lots of greens, then I could see how bacteria could start to grow, and actually how the water could get a little stale, which would not encourage drinking.
I just discovered something w(this is sort of off the subject, but it's about water) Since we hadn't gotten a water filter yet put on the new kitchen sink, we bought bottled water, and I filled up their bottles and crocks with that. They drank so much water, I couldn't believe it. At first I thought it was just the stress of moving, and they were dehydrated, and when I changed from bottled water to regular water, they went back to their normal habits. But then to test out if it was the water, I offered bottled water again, and sure enough, the drinking parade began.
Either they are picky bunnies, or I am worried about the water we drink here in the Bay Area (even when using a sink filter) Can the bunnies smell something funky/harmful in the water....hmmmmmmmmmm.