Be honest and tell them that you are a Nikkei jin . You might get a better treatment than you expected.
@Keihan can probably attested to that.
Affirmative, you will be treated significantly better than other gaijin and precisely because you told them you're nikkei. Trust me, at "N3ish" level I'm guessing you didn't grow up in a Japanese-speaking household so by the third syllable out of your mouth, tencho will know you're not a true-blue Cousin of Tojo. And then as others have pointed out, your clothing, your gait, basic body language, unless you've spent years in Japan and are extremely talented at mocking them, will give you away in an instant. Just think of the "three glasses" bar scene in Inglourious Basterds.
In my case, my accent has always been pretty spot-on, my actual command has always bordered on shitty-messy because I truly don't care to improve but I can still get around fine. That said, whenever I approach a shop/tencho the first thing I do is announce myself as a Japanese-American and ask if that's going to be ok. Very rarely, tencho will find this intriguing and ask a few questions about my family background while escorting me into the shop; the other 95% of the time, especially in Tokyo, I just get a look of indifference while being escorted into the shop. I've never been turned away from any establishment, ever. That said, I've been with half-Japanese friends who were completely fluent in Japanese but were instantly arm-crossed by the tencho. At the end of the day, Japan will always be Japan, and there's no substitute for a Japanese face.
But yeah, bottom line...don't attempt to fake it because it won't work. Just tell the truth and you'll be fine.
