气 basically means the atmosphere here, so 气温 means the temperature of the atmosphere, or the weather.
温度 means temperature, so just the number you get.
Body temperature is 体温。我的体温是多少(度)?What is my body temperature?
外面温度很高。The temperature outside is very high.
今天气温很高。The weather today is really hot (high temperature).
Hope that helps!