Many different types of injury can occur while someone is running. Although a certain amount of stiffness plus sore and tightened muscles is normal when training, it shouldn’t last for days and days on end.
As in the case of any kind of sports injury, correct diagnosis is fundamental to successful recovery. Check whether the problem is caused by inappropriate or poor quality running shoes - a very common issue specially here in NYC, poor or bad nutrition or insufficient preparation. Also keep in your mind that even when your injury has healed, it will take time and patience to get back to your normal.