I'm probably pretty late to the party but ill break it down a bit, unfortunately most of japan is seen as Xenophobic by most of the general population, but as for any country, the collective opinion will vary depending on location.
Tokyo(for example) receives many visitors, they are used to foreigners and will often be more curious as opposed to guarded around them. you can expect warm receptions from Tokyo, but as with any capitol both good and bad people are attracted to it, so it is not impossible to have a couple bad encounters.
Okinawa (places further up or down, rural(i would think works here)) you'll most likely get fewer and fewer formalities, they will not be used to foreigners and judge based on stereotypes, and sadly negative stereotypes live longer and stronger than positive, though it doesn't mean that you will always get bad receptions, though there are places where that is so, as small as they may be.
It will also be determined by the generation gaps, youths of this generation around the world are far more tolerant and understanding than the adults/seniors of 40+ years ago.
Your nationality, skin tone, how you present yourself, how much understanding of Japanese culture you have and how you present your understanding, among others, are also factors here. But they are minor or major depending on where, again, your going.
You'll have an easier time than me, albeit I've yet to visit japan itself i have lived and interacted with enough Japanese resident/tourist since living in Hawaii to be able to confirm it first hand. I am both black and American, though as far as i can tell, they do not resent blacks, it seems to have a more fear based view of them(a view I've collected from a number of stereotypical Japanese entertainment, a massively buff current/ex-soldier, bald may/not where glasses/shades towering in height, though the only thing i have in common with that is height (6.2-.3 in height) i do know from experience how intimidating people have found me from my height alone) it doesn't help my landlord is is a ra... who keeps telling me to give up on japan, that they wont like me (emphasizing on there Xenophobic behavior) but i still want to go, being the fan that i am of Japanese(and Korean) media and games, i really want to get into the industry.
If you have the chance you might as well throw cation to the wind and go, take in both negative and positive as a learning experience, and learn how to make your place, from it, into japan. The positive always outweighs the negative and Japan is a place worth a bit a hardships(for me it is).