You can't go wrong with either one. Waimanalo has a beautiful beach and will be less crowded; however, your choices for rental properties will be significantly fewer. Another factor is restaurants. Although, it's not that far from Kailua, you will have a longer drive to access the town and all of the restaurants. If you're going to eat most of your meals at the house, it's a moot point.
Does Waimanalo have more crime than Kailua? Probably, due to the demographics of the area...but it's not a whole lot more. Most of the local people are very welcoming. If you respect them and the land, they will respect you. Always a few bad apples, but you find that anywhere.
I personally love Kailua because it's where I grew up and I like the ability to go into town quickly when I need to. Waimanalo has far fewer stores.
Bottom line, I wouldn't hesitate to recommend Waimanalo to a friend, but my personal choice is Kailua.