They both have their own strengths & weaknesses. Both villains created themselves using their intellect. I would have to say The Thinker is smarter, but Eobard Thawne has technology and the Future at his side. It’s literally his whole gig, a superhuman brain.

For example, The Thinker needed to rely on Ralph Dibny as a host to face-morph, whereas Reverse-Flash can simply use his appearance-stealing cord device to copy somebody's appearance (approx. 30 years later he still retains the appearance of Earth-1's Wells, although his hair is becoming blonde again).

And the way the showwriters did our boi genius in Season 4... idk dude. At least Reverse-Flash is smart enough to be alive, unlike The Thinker.