Bagel is a Jewish bread very popular in NYC and its surroundings. It is not so easy to find in supermarkets in Europe and it is same in Japan too.
It is interesting that major Japanese bakeries do not bake bagels at their factories. Therefore bagels can be found at small local bakeries. However, local bakeries which sell typical Japanese breads and pastries do not sell bagels. Or may be they sell small portions of bagels but the quality is unfortunately not high.
Therefore if you are looking for a nice bagels, you should better to search bakeries which sell bagels only. This is as same as in NYC where store which sells nice bagels do not sell other bread or pastry.
Then, the difference between US and Japanese bagels are that bagels in US are much simple than in Japan. Usually there are several flavors such as plain, onion, garlic, sesame and everything in US but Japan sells savory and sweet bagels such as filled with chicken, fruits and cream.