26 yo female with severe knee and hand pain in the morning along with pain on balls of feet. Pain also in middle of night. Possible RA or Lyme disease?

Anything is possible. No need to speculate. Go see your family doctor for evaluation, testing & treatment options. S/he can refer you to a rheumatologist if necessary.
Possible. Rheumatology work up is needed, including a discussion with your doctor, as well possible blood tests. There are more than 1 or 2 conditions that could be ruled out on the systemic level.