Both of the crashes mentioned by MPH were approach crashes - not cruise.
Another thunderstorm-related cruise-phase (of sorts) accident was the Braniff BAC111 accident in Nebraska on August 6, 1966.
The captain had reverted to a widely used piston strategy, and chose to descend to a very low cruise alt (less than A100) in order to mitigate the effects of a severe squall line that was across his route.
A farmer was watching the lightning show, saw the jet fly overhead and into a roll cloud. He heard a loud bang, then saw the aircraft descend rapidly to the ground and explode. Turns out that the horizontal stab broke away from the aircraft due to overload.
There were a few jet crashes attributed to thunderstorm encounters in the 'early' years of their introduction - mainly in the critical take-off/landing phase. Another was a B707 that took off out of Miami and flew into a cell.
But not too many during cruise.