Flying was an ambitious record, but it also seemed like he was being pressured to be more mainstream. It was his "Sex and Religion" moment, which is also a great record. He bounced back really nicely with "The Extremist". Surfing takes it for me, one of the greatest instrumental guitar records of all time.
I'm a Satch freak, so choosing is painful. Of the two, I like the songs on Surfing With the Alien better, but I like the guitar tones more on Flying In A Blue Dream. I voted "Surfing" but only by a tiny margin.