There isn't a best restaurant in Bergamo :)
I agree with SirCharly: in the Old Town, Da Mimmo is a good choice for a pizza or a traditional dinner. Alternatives can be Da Franco (just in front to Mimmo) or Ristorante San Vigilio.
A couple of km out of the center there is "La Grotta Azzurra", with a really good food. about 8 years ago