As someone with 2 aging, often sore knees who has done a fair amount of pool running...what works best for me is 45-90 minutes of freestyle with a pull buoy the whole time. Don't let the knees do anything.
Pool running feels okay in the water but can irritate your knees, even though it is not weight bearing. You actually twist your joint a lot if you are not very careful, with heavy resistance in the water. This can cause even more pain.
After pulling freestyle for a few weeks, you'll start to get decent at it and have the side benefit of improved shoulders and pecs. You may lose a bit of fitness as you get better, but eventually you will be able to do very hard, longer swim workouts this way. Either way your running fitness will diminish to a degree, but your injury won't be irritated.
All IMO.