Various hideouts are the best friends of any assassin, letting you sneak to your victim or lose a pursuit. Below you will find a list of "disappearing" methods available in AC III.
Haystacks - hay piles which you may know from the previous installments are very common in Boston and its peripherals. Just run into them and Connor will automatically jump inside. You can also hide in hay transported on carts. That way you can pass by road patrols unnoticed.
Wells - they work just as hay piles, but you can move along their ledges.
Crowds - if you see a group of 3-4 people standing beside each other, approach them slowly and mix into the crowd. Likewise, you can "disappear" by standing beside people leaning against a hedge or wall of a building or by sitting on a bench.
Building interiors - as you're trying to lose a pursuit, you may come across doors leading inside various buildings. Head inside and Connor will quickly get through the apartment and exit onto the street on the other side. It's a very useful shortcut thanks to which you can quickly lose a pursuit.
Bushes - dense and tall bushes which grow between trees and beside stream shores can be used to hide as well. Just get inside them slowly and Connor will quickly disappear from the sight of the pursuit. Just remember that you will exit your hideout when you start running.
Water - while you're in a harbor or by a river shore, it's easiest to hide underwater. In order to dive, pres the interaction button. You can move while underwater, but remember that Connor will eventually swim to the surface to breathe in and won't be able to dive back for some time.