I'm originally from the Boston area. My wife, MrsTokyoKid, is Japanese. We live in the Nagoya area. We fly to Boston to visit family and friends twice a year. When we return, our suitcases are full of presents for Japanese family, friends, and colleagues at work. Here's a list of gift ideas to bring with you to Japan for your host family (keep in mind these are Boston/New England presents but you could easily adapt them to your region of the U.S.):

1) Harvard University/Boston Red Sox T-shirts & caps (Matsuzaka & Okajima play for the team)
2) Jam - We always bring back some Stonewall Kitchen blueberry jam since Maine is famous blueberries. Be sure to wrap in bubble wrap and stick it inside a zip lock bag in case the jar breaks.
Do not put it in your carry on as jam is considered a liquid!
3) Coffee - Again, we always bring back coffee from Green Mountain Coffee located in Vermont (who knew Vermont was famous for its coffee beans, eh? LOL). The blends we choose are Harvard, Vermont, and Nantucket. For flavored coffee we choose blueberry (seasonal). For myself, I bring back blueberry, coconut,
pumpkin spice, chocolate raspberry truffle, & cinnamon swirl. Outside of New England, flavored coffees are apparently not popular. If coffee isn't your thing, substitue it with interesting tea which can only be found in your neck of the woods. Japanese people drink a lot of tea and coffee especially when someone comes to the house.
4) Cookies, candy, & chocolate - If there are any unique to your area, bring them. Your host family will serve them with tea/coffee whenever visitors arrive at the house (announced and unannounced). CAUTION: Avoid bringing chocolate during the summer months (June through September)!!! It's incredibly hot and humid
throughout most of Japan and the chocolate will must likely resemble chocolate soup by the time your host family receives it. This advice comes from personal experience. Fortunately, the chocolate was for us and was never intended as a gift. Whew!!
5) Local crafts, pottery, etc. - In the Boston area we have Dedham Pottery.
6) Any interesting and unique jars/bottles/packages of ketchup, mustard (I love honeycup mustard and so does my entire family including my mother-in-law!), salad dressing, onion dip, garden vegetable dip,
pancake mix, maple syrup, and soup. You'll have to show your host family how to make whatever you bring. The metric system is used here. Before you leave home, print out metric conversions. This will
make the cooking process considerably easier!!

Again, be careful with glass and anything considered "liquid" by the TSA in your carry on. If you have any doubt, check their website before you buy the present.

Whatever your bring keep in mind most Japanese homes are small and there's not a lot of space for big items. Keep the size of the presents small. It will be easier for you to pack and transport, too. Bring gift wrapping paper with you in your suitcase (the small square sheets) which you can use after arriving in Japan. It will be less of a hassle dealing with security and the gift wrapping will arrive in your host family's hands without any rips and not looking like it had a rough journey half way around the world. I hope these suggestions help.

Have a great time in Japan! It's an amazing country. That's why I live here now with MrsTokyoKid and BabyTokyoKid. The first time I came to Japan as a university student I was bitten by the Japan bug and found myself returning year after year after year until moving here with the wife and child. I miss Boston but being able to live in Japan is wonderful, too!