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@BringMeMyFix
It sounds like patellar tendonitis, which is a transient thing if you take the right action.
Get some RICE (rest, ice, compression, elevation), don't leap on your bike and start doing stressful accelerations the minute you leave home/work.
Cover up your knees - it's chilly now.
Be very mindful of your 'form' on the bike - try to keep your knees tracking straight, stand up and use your bodyweight to ease away from standing starts, rather than thrashing it (sitting or standing). Use a brake to slow down, at least until the pain subsides.
That's my guess/advice.