Use kayak or Google flights to search for flights, but book directly through the airline. Do not book flights through a third-party website - it can end up being a real PITA.
Also, make sure you know about any hidden fees or other potential problems before choosing and airline. Some smaller airlines can seem like a great deal, but they nickel and dime you to death. Another problem with smaller airlines can be limited flights. If a particular airline only fly's out of your airport once or twice a week, it can be a real problem if your fight gets cancelled for some reason since you won't be able to get another one until the next scheduled flight.