Is this for the best pokemon like it says in the title or your favorite? This isn't exactly clear...
That being said, you can make a case for any generation. 2nd Generation introduced walling supremeacy no other generation will ever be able to topple (Suicune, Blissey, Forretress, Donphan, Skarmory, etc.) and had other amazing pokemon like Heracross, Tyranitar, Celebi, and Raikou.
1st generation was the original, and had a few powerhouses itself (Rhydon, Gengar, Alakazam, Starmie, Machamp, Snorlax, Zapdos, Marowak, Chansey, Tauros, etc.) and all the awesomeness that comes with it being the original game. Still, it just doesn't stack up to the power of the 2nd generation pokemon.
3rd Generation introduced some good ones (Salamence, Metagross, Regice, Milotic, Swampert, Dusclops, Medicham, etc.) However, it didn't really bring much else to the table, besides maybe newer graphics lol.
4th Gen probably gives 2nd the best run for its money. However, with all the evos, I'm only going to count pokemon who were terrible until they evolved. Other pokemon who were good before evolving are going to be left out. However, stuff like Tangrowth, Garchomp, Cresselia, Heatran, Azelf, Ambipom, Hippowdon, Infernape, and Weavile make 4th gen pretty stellar.
It's between 2md and 4th for me, and IMO it's second or else the game would be so so so much different without that generation.