Moltres has better defenses than Entei, and a higher Sp. Atk to use for it's fire. Entei only has a tiny advantage on Attack, and a bit more HP and speed than Moltres. I still think Moltres is a bit better, though it's close.
Regardless, Mewtwo, Groudon, Lugia, and Deoxys (FR/LG) are the best. Other good ones include Rayquaza, Kyogre, Raikou, Latios, and Zapdos.