At the moment the iPhone 6s / 6s Plus and the SE are the best.
The SE is basically the iPhone 6s / 6s Plus but in the shell of an iPhone 5s.
While the SE doesn't get some things like the 2.0 fingerprint sensor, or 3D Touch, I prefer it over the 6s or the 6s Plus. I love the look of the 5s, and think the SE is a great new phone in an old phones skin.
Although come September the iPhone 7 and 7 Plus will be released, and we'll probably see better specs in them, as well as maybe some new features that are exclusive to them, and they'll be faster and more advanced than the 6s or 6s Plus. So if you're in the market for an iPhone, I'd wait until WWDC (around June) when the iPhone 7 and the 7 Plus are announced, to see if you'd prefer them.
Although personally I think I'll still end up favoring the size and look of the SE.