I had a PAP and HPV test 2 years ago that came back negative. I have only been sexually active with my boyfriend during that last 3 years. Now my boyfriend of 3 years has been diagnosed with HPV due to a genital wart. Is it possible that he had HPV prior to 3 years ago given my negative test only 2 years ago?

Sure... you said YOU was tested... you didn't say HE was tested. Its also pssible you contracted it before being tested, short enough time that you tested negative at the time of the test. It doesn't result in an instant positive immediately after exposure.