I wasn't around in 1990 (I mean, I was there, but did not see all eligable movies back then) so I can't realy judge in hindsight if his performance was oscar worthy.
but I thought the exact same thing this afternoon, when watching Casino (where he simply reprises his Tommy D character).
one actor that didn't deserve to win OVER him is Andy Garcia though, who was nominated as well in that category. I think he does great in GF III but Pesci is way better even though his role was a lot about swearing and kicking.
other good movies that year were Awakenings, Dances with Wolves, Edward Scissorhands and Millers Crossing