Been there - get a gait assessment, stretch ALL the leg and foot tissues often (Quads, Hams, Calves, PF, hip flexors, IT Band), learn to use a foam roller and lacrosse ball, get some PT to help you with stretching, massage and healing if you need, build leg strength. Might give your distance shoes a look also. I threw away all my old thick heel shoes after going to a Crossfit Endurance seminar and went totally minimal (Vibrams and New Balance Minimus). This worked really good for me for shorter runs, but I ended up with a stress fracture on a distance run. I now use a minimalist shoe with a thicker sole for distance. I think they are the Saucony brand.

Try icing your knee a couple of times a day

I suffered for many years until I found squats. Google for "Stumptuous" and "mistressing the squat". Krista is my savior, truly.

Its probably related to body postion when you run. I'd look for a trainer to watch and evaluate your running form.

I had some issues similar to this when I was getting back on the running saddle and was advised to do some strength training for my quad. Went through about 6 weeks of therapy and not running and was able to come back even stronger than before. Plus I started crossfitting after and it hasn't bothered me since.

Of course, you should always seek guidance from a medical professional as well :)

I have knee problems, but it seems to be less when I don't stretch my knees the wrong way. So far not pulling my foot up behind my rear end seems to be not making it worse.

I have bad knees from running one too many miles for Uncle Sam. If they are really bothering you then get in to see an orthopedist. I started having issues while preparing for an Army 10 miler and I had to completely stop training. The problem was the inside of my knee was essentially acting like a brillo pad and scraping against the tissue. A good X-Ray will help ensure you do not do more damage to the knee. I can still run, but on a treadmill and I have to keep it to about two miles. Eventually I will have to go the store and buy new knees (kidding about the store part), but I know the score. Seriously, you knees are nothing to blow off and ignore.

I second the foam rolling, icing the knee, getting a gait analysis, etc. The fact that it doesn't bother you when you sprint makes me think you could be heel-striking too much and taking too big of strides when you run longer distances. Try taking shorter strides and aim to strike between the middle (arch) of foot and heel (rather than heel first).

I know it isn't a cure-all, but I just started drinking bone broth to help my tendonitis and I am shocked how much better it feels after only a week. Other joint aches and pains are gone or significantly better as well :)

Slow down if you are trying to do 5-6 milers at the same speed as you sprints. 5-6 miles is a short run so if 5-6 miles is a long run compared to the 1 mile and shorter sprints that you are doing then you are probably increasing your mileage too fast. Most coaches recommend for distance running to increase no more than 10% distance a week, so hack your mileage, slow down and definitely look into a more minimalist shoe. I just can't go there with the Vibram 5 finger fan camp, however, I do believe there are some important points there. I use a cross country racing flat, Nike Zoom xc3 and they are super light. For long distances a heavy shoe will start to wear on you from its sheer weight, let alone its high heeled design and whatever mud or moisture you are picking up as you are trotting along. Also, are you a city pavement runner or trail runner, going hard down hills? Someone above mentioned going at it on a softer course and that is something I'd look at too.