Length. How long have you felt "under the weather?" if only sick a couple of days or up to a week, it could be a cold (less likely the flu). The flu has many symptoms and usually includes a fever, chills, muscle aches, etc.. (very sick). Allergies are a constant or if they never go away or return the same time every year.
Timing and degree. Sometimes it is hard to tell. To briefly summarize i will describe the general symptoms of each flu: the most obvious- very sudden onset high fevers, severely ill, severe muscle aches, sweats, lasts 1-2 weeks- will almost always need to miss work cold: stuffy nose, thicker mucous, cough , sore throat , faily sudden onset. Allergies: slower onset, runny mucous, itchy nose, itchy eyes, dry cough.
Depends on symptoms. Cold and flu symptoms will usually have systemic symptoms like fever, chills, muscle pain. A "cold" that lasts for more than a week is probably a sinus infection. Seasonal allergies are usually "seasonal" and symptoms include watery, itchy eyes, runny nose, coughing, sneezing, and sometimes a sore throat.