If you recall having similar symptoms or discomfort prior to your cycling training years, it might suggest another cause - but surely improper cycling or rowing form might aggravate the issue over time. Hard to say and i’m not knowledgeable in orthopaedics.
A few years ago, I was experiencing pain in the area “behind” my knee, possibly from PCL or hamstring ligament. I met Dr. Keith Bush at the London Clinic who in addition to being an associate of the GB rowing team had the right specialty. At that time my only sports focus was rowing and weight lifting. Aside from the consultation and help I got (the pain passed after some time and rest) I do recall him warning me about deadlifts - which I eventually substituted for leg press exercises at the gym. I suspect my knee pain had to do with improper form given a steep load progression in the gym. Therefore i constantly come back to form. Like I mentioned above, rowing itself should not cause knee pain and so shouldn’t biking. Comparing them your feet and hips are in a far more locked position on the erg than on a bike. Therefore, in my humble opinion, there’s greater risk for improper form on a bike than on an erg. Yesterday’s TR workout incorporated some quadrant drills and Coach Chad’s subtitles mentioned something about being observant of knee discomfort, so it seems to be an omnipresent focus and very good that TR highlight form in their trainings. If you just find rowing boring over 20 mins, then there’s not much to do 
pick something else mate!
Workouts: If you’re already on an intense cycling program, i wouldn’t substitute any of the intense cycling workouts with erg sessions. Choose a specialty and focus on it, be it rowing or cycling. However I find longer endurance sessions far more enjoyable on an erg than on the trainer, unless cycling outside of course. The Pete Plan was mentioned in this thread and it’s an excellent plan, however it would be far too taxing to combine with any TR program. Therefore I recommend the beginner plan. Make yourself an excel spreadsheet with space for up to 3x workouts per week. In the columns log Date / Goal Meters / Attempted Pace / Actual Pace / Total Meters Rowed. The pace will be your split time / 500m, on the upper-right corner of the S4 monitor - just make sure it’s over 500m and not any other distance. Stroke rate will be variable depending on workout. Start slow, i.e. 17-20 average to begin with and focus only on form. Gradually increase over time, when your body starts to “learn” the motion and form builds. I’m also using a Waterrower at home, and whilst the stats aren’t comparable with C2, all your rowing and progression is relative to the brand you’re using, although the C2 is probably more accurate to “real” rowing in how it measures things. The Waterrower is far more enjoyable to row on imo. You could get far better smartrow and omit the S4 montor, but maybe not worth it depending on your priorities.
If you just want to row sometimes, this is my hour workout: 5-10 min warmup in the 18-21 spm range. Then increase your stroke rate by 1 spm every minute, until you reach somewhere around 27-32. You need to evaluate your RPE to gauge how intense it gets and when to stop increasing, but don’t go into a too high zone (avoid messing with your cycling plan). Then back off the SPM in the same rate you increased it. Repeat for as many cycles as you like. I usually make 4-6 cycles or approx. an hour’s rowing. It’s a good workout as it incorporates low and higher intensity and trains your ability to maintain stroke rate. It requires some focus but isn’t mentally taxing.
Form: Dark Horse Rowing on Youtube has many good technique sessions. I prefer to row with low converse all stars on the Waterrower. Avoid wearing a shoe with a big drop, and start with a neutral position. Make sure to put the strap over the widest part of your foot.
