Let's not discount McGwire's shocking domination of baseball during his five year stint in St. Louis. His numbers in Oakland alone are pretty close to Ramirez'.
Steroids and everything, I would put Manny ahead of McGwire.
Definitely not ahead of Pujols. Manny has had three years where his numbers have surpassed Pujols' career average. Insanity. I would have loved to see Pujols taking shots at the Green Monster in his prime. However, you are absolutely correct when you talk about Pujols' and the AL. In a 423 AB sample, Pujols has hit .350 in interleague play, with a slight drop in power. His OPS is still a robust 1.036, which still has him comfortably ahead of Ramirez.