It is a bit dependent on which ace, but generally speaking the best boss killer without competition is Eagle. The laser beam just melts through almost anything.
Flamer is good if you have the nerve to get up close.
Generally speaking avoid the following for boss fights: Blitzer (at least single/few target bosses like Red Queen, well handled it works fine against e.g. Doom, Gun Head, 100, 120), Sparrow, Phoenix, Defender, Dragon, Zapper, and Havoc.